5DM6
Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth 0] | SCOP2 Family | Ribosomal protein L1p/L10e-like | 8065335 | 4002929 | SCOP2 (2022-06-29) |
A [auth 0] | SCOP2 Superfamily | Ribosomal protein L1p/L10e-like | 8065336 | 3001911 | SCOP2 (2022-06-29) |
B [auth A] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8038538 | 3000135 | SCOP2B (2022-06-29) |
B [auth A] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8038534 | 3000334 | SCOP2B (2022-06-29) |
C [auth B] | SCOP2B Superfamily | Translational proteins | 8038543 | 3000811 | SCOP2B (2022-06-29) |
D [auth C] | SCOP2B Superfamily | Ribosomal protein L4 | 8038546 | 3001146 | SCOP2B (2022-06-29) |
E [auth D] | SCOP2B Superfamily | RL5-like | 8038549 | 3001709 | SCOP2B (2022-06-29) |
F [auth E] | SCOP2B Superfamily | Ribosomal protein L6 | 8038556 | 3000724 | SCOP2B (2022-06-29) |
F [auth E] | SCOP2B Superfamily | Ribosomal protein L6 | 8038552 | 3000724 | SCOP2B (2022-06-29) |
G [auth F] | SCOP2B Superfamily | Ribosomal protein L11, C-terminal domain | 8033402 | 3001186 | SCOP2B (2022-06-29) |
G [auth F] | SCOP2B Superfamily | Ribosomal L11/L12e N-terminal domain-like | 8033405 | 3000950 | SCOP2B (2022-06-29) |
H [auth G] | SCOP2B Superfamily | Ribosomal protein L13 | 8038555 | 3001134 | SCOP2B (2022-06-29) |
I [auth H] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8038558 | 3000433 | SCOP2B (2022-06-29) |
J [auth I] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8038561 | 3001045 | SCOP2B (2022-06-29) |
K [auth J] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8038562 | 3000884 | SCOP2B (2022-06-29) |
L [auth K] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8038564 | 3000995 | SCOP2B (2022-06-29) |
M [auth L] | SCOP2B Superfamily | Translational machinery components | 8038566 | 3000571 | SCOP2B (2022-06-29) |
N [auth M] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8038569 | 3000334 | SCOP2B (2022-06-29) |
O [auth N] | SCOP2B Superfamily | Ribosomal protein L20 | 8038571 | 3000563 | SCOP2B (2022-06-29) |
P [auth O] | SCOP2B Superfamily | l21p-like | 8038572 | 3002005 | SCOP2B (2022-06-29) |
Q [auth P] | SCOP2B Superfamily | Ribosomal protein L22 | 8038576 | 3001078 | SCOP2B (2022-06-29) |
R [auth Q] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8038577 | 3000210 | SCOP2B (2022-06-29) |
S [auth R] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8038578 | 3000334 | SCOP2B (2022-06-29) |
T [auth S] | SCOP2B Superfamily | Ribosomal protein L25-like | 8038580 | 3001161 | SCOP2B (2022-06-29) |
U [auth T] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8038582 | 3000539 | SCOP2B (2022-06-29) |
V [auth U] | SCOP2B Superfamily | L28p-like | 8038585 | 3001966 | SCOP2B (2022-06-29) |
W [auth V] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8038586 | 3000713 | SCOP2B (2022-06-29) |
X [auth W] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8038590 | 3001378 | SCOP2B (2022-06-29) |
Y [auth Z] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8038593 | 3001320 | SCOP2B (2022-06-29) |
Z [auth 1] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8038526 | 3001320 | SCOP2B (2022-06-29) |
BA [auth 3] | SCOP2B Superfamily | L35p-like | 8038530 | 3000790 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth 0] | Ribosomal_L1_2nd_1 | e5dm601 | A: a+b two layers | X: a+b domain in Ribosomal protein L1 (From Topology) | H: a+b domain in Ribosomal protein L1 (From Topology) | T: a+b domain in Ribosomal protein L1 | F: Ribosomal_L1_2nd_1 | ECOD (1.6) |
A [auth 0] | Ribosomal_L1_1st | e5dm602 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Rossmann-like domain in Ribosomal protein L1 (From Topology) | T: Rossmann-like domain in Ribosomal protein L1 | F: Ribosomal_L1_1st | ECOD (1.6) |
B [auth A] | Ribosomal_L2_1 | e5dm6A2 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_L2_1 | ECOD (1.6) |
B [auth A] | Ribosomal_L2_C | e5dm6A1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L2_C | ECOD (1.6) |
C [auth B] | Ribosomal_L3 | e5dm6B1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L3 | ECOD (1.6) |
D [auth C] | Ribosomal_L4 | e5dm6C1 | A: a/b three-layered sandwiches | X: Ribosomal protein L4 (From Topology) | H: Ribosomal protein L4 (From Topology) | T: Ribosomal protein L4 | F: Ribosomal_L4 | ECOD (1.6) |
E [auth D] | Ribosomal_L5_C | e5dm6D1 | A: a+b two layers | X: Ribosomal protein L5 (From Topology) | H: Ribosomal protein L5 (From Topology) | T: Ribosomal protein L5 | F: Ribosomal_L5_C | ECOD (1.6) |
F [auth E] | Ribosomal_L6 | e5dm6E2 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: Ribosomal_L6 | ECOD (1.6) |
F [auth E] | Ribosomal_L6_1 | e5dm6E1 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: Ribosomal_L6_1 | ECOD (1.6) |
G [auth F] | Ribosomal_L11 | e5dm6F1 | A: alpha arrays | X: HTH | H: HTH | T: Ribosomal protein L11, C-terminal domain | F: Ribosomal_L11 | ECOD (1.6) |
G [auth F] | Ribosomal_L11_N | e5dm6F2 | A: a+b two layers | X: Ribosomal protein L11/L12e N-terminal domain-like | H: Ribosomal protein L11/L12e N-terminal domain (From Topology) | T: Ribosomal protein L11/L12e N-terminal domain | F: Ribosomal_L11_N | ECOD (1.6) |
H [auth G] | Ribosomal_L13 | e5dm6G1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal protein L13 and L16-A (From Topology) | T: Ribosomal protein L13 and L16-A | F: Ribosomal_L13 | ECOD (1.6) |
I [auth H] | Ribosomal_L14 | e5dm6H1 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: Ribosomal_L14 | ECOD (1.6) |
J [auth I] | Ribosomal_L27A | e5dm6I1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal proteins L15p and L18e (From Topology) | T: Ribosomal proteins L15p and L18e | F: Ribosomal_L27A | ECOD (1.6) |
K [auth J] | Ribosomal_L16 | e5dm6J1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal protein L10e | F: Ribosomal_L16 | ECOD (1.6) |
L [auth K] | Ribosomal_L17_1 | e5dm6K1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Prokaryotic ribosomal protein L17 (From Topology) | T: Prokaryotic ribosomal protein L17 | F: Ribosomal_L17_1 | ECOD (1.6) |
M [auth L] | Ribosomal_L18p | e5dm6L1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_L18p | ECOD (1.6) |
N [auth M] | Ribosomal_L19 | e5dm6M1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L19 | ECOD (1.6) |
O [auth N] | Ribosomal_L20 | e5dm6N1 | A: alpha arrays | X: PABP domain-like | H: Ribosomal protein L20 (From Topology) | T: Ribosomal protein L20 | F: Ribosomal_L20 | ECOD (1.6) |
P [auth O] | Ribosomal_L21p | e5dm6O1 | A: beta barrels | X: Ribosomal protein L21p (From Topology) | H: Ribosomal protein L21p (From Topology) | T: Ribosomal protein L21p | F: Ribosomal_L21p | ECOD (1.6) |
Q [auth P] | Ribosomal_L22 | e5dm6P1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Ribosomal protein L22 (From Topology) | T: Ribosomal protein L22 | F: Ribosomal_L22 | ECOD (1.6) |
R [auth Q] | Ribosomal_L23_2 | e5dm6Q1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal proteins S24e, L23 and L15e (From Topology) | T: Ribosomal proteins S24e, L23 and L15e | F: Ribosomal_L23_2 | ECOD (1.6) |
S [auth R] | ribosomal_L24_1 | e5dm6R1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: ribosomal_L24_1 | ECOD (1.6) |
T [auth S] | Ribosomal_L25p | e5dm6S1 | A: beta barrels | X: Ribosomal protein L25-like | H: Ribosomal protein L25-like (From Topology) | T: Ribosomal protein L25-like | F: Ribosomal_L25p | ECOD (1.6) |
T [auth S] | Ribosomal_TL5_C_1 | e5dm6S2 | A: a+b complex topology | X: Ribosomal protein TL5/L25 C-terminal domain-like | H: Ribosomal protein TL5/L25 C-terminal domain-related (From Topology) | T: Ribosomal protein TL5/L25 C-terminal domain-related | F: Ribosomal_TL5_C_1 | ECOD (1.6) |
U [auth T] | Ribosomal_L27 | e5dm6T1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal L27 protein | F: Ribosomal_L27 | ECOD (1.6) |
V [auth U] | Ribosomal_L28 | e5dm6U1 | A: few secondary structure elements | X: Ribosomal protein bL28-related (From Homology) | H: Ribosomal protein bL28-related | T: Ribosomal protein L28 | F: Ribosomal_L28 | ECOD (1.6) |
W [auth V] | Ribosomal_L29 | e5dm6V1 | A: alpha bundles | X: Long alpha-hairpin | H: Ribosomal protein L29 (L29p) (From Topology) | T: Ribosomal protein L29 (L29p) | F: Ribosomal_L29 | ECOD (1.6) |
X [auth W] | Ribosomal_L30 | e5dm6W1 | A: a+b two layers | X: Ribosomal protein L30p/L7e (From Topology) | H: Ribosomal protein L30p/L7e (From Topology) | T: Ribosomal protein L30p/L7e | F: Ribosomal_L30 | ECOD (1.6) |
Y [auth Z] | Ribosomal_L32p | e5dm6Z1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L32p | ECOD (1.6) |
Z [auth 1] | Ribosomal_L33 | e5dm611 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L33 | ECOD (1.6) |
AA [auth 2] | Ribosomal_L34 | e5dm621 | A: extended segments | X: 50S ribosomal protein L34 (From Topology) | H: 50S ribosomal protein L34 (From Topology) | T: 50S ribosomal protein L34 | F: Ribosomal_L34 | ECOD (1.6) |
BA [auth 3] | Ribosomal_L35p | e5dm631 | A: a+b two layers | X: Ribosomal protein L35p (From Topology) | H: Ribosomal protein L35p (From Topology) | T: Ribosomal protein L35p | F: Ribosomal_L35p | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth 0] | PF00687 | Ribosomal protein L1p/L10e family (Ribosomal_L1) | Ribosomal protein L1p/L10e family | This family includes prokaryotic L1 and eukaryotic L10. | Domain |
B [auth A] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | - | Domain |
B [auth A] | PF00181 | Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2) | Ribosomal Proteins L2, RNA binding domain | - | Domain |
C [auth B] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
D [auth C] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
E [auth D] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | - | Domain |
E [auth D] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
F [auth E] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | - | Domain |
G [auth F] | PF03946 | Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N) | Ribosomal protein L11, N-terminal domain | The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. | Domain |
G [auth F] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | - | Domain |
H [auth G] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
I [auth H] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain |
J [auth I] | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | - | Family |
K [auth J] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | - | Domain |
L [auth K] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
M [auth L] | PF00861 | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast (Ribosomal_L18p) | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast | - | Family |
N [auth M] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
O [auth N] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
P [auth O] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
Q [auth P] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
R [auth Q] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
S [auth R] | PF17136 | Ribosomal proteins 50S L24/mitochondrial 39S L24 (ribosomal_L24) | Ribosomal proteins 50S L24/mitochondrial 39S L24 | - | Family |
S [auth R] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
T [auth S] | PF14693 | Ribosomal protein TL5, C-terminal domain (Ribosomal_TL5_C) | Ribosomal protein TL5, C-terminal domain | This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, Pfam:PF01386. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC pr ... | Domain |
T [auth S] | PF01386 | Ribosomal L25p family (Ribosomal_L25p) | Ribosomal L25p family | Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress. | Domain |
U [auth T] | PF01016 | Ribosomal L27 protein (Ribosomal_L27) | Ribosomal L27 protein | - | Family |
V [auth U] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
W [auth V] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
X [auth W] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
Y [auth Z] | PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family |
Z [auth 1] | PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family |
AA [auth 2] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
BA [auth 3] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |