RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Enzyme Classification Number = 3.1.1.29

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 182 Structures.

Refinements

Structure Determination Methodology

experimental (182)

Scientific Name of Source Organism

	Homo sapiens (79)
	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (29)
	Sus scrofa (13)
	Escherichia coli K-12 (10)
	Pseudomonas aeruginosa PAO1 (9)
	Mycobacterium tuberculosis H37Rv (7)
	Vibrio cholerae O1 biovar El Tor str. N16961 (7)
	synthetic construct (7)
	Mycolicibacterium smegmatis MC2 155 (5)
	Thermus thermophilus HB8 (4)

More...

Taxonomy

	Bacteria (92)
	Eukaryota (88)
	Archaea (8)
	other sequences (7)
	unclassified sequences (1)

Experimental Method

	ELECTRON MICROSCOPY (91)
	X-RAY DIFFRACTION (84)
	SOLUTION NMR (7)

Polymer Entity Type

	Protein (182)
	RNA (92)
	DNA (2)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (15)
	1.5 - 2.0 (34)
	2.0 - 2.5 (25)
	2.5 - 3.0 (28)
	3.0 - 3.5 (35)
	3.5 - 4.0 (23)
	4.0 - 4.5 (7)
	> 4.5 (5)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (5)
	2005 - 2009 (10)
	2010 - 2014 (37)
	2015 - 2019 (38)
	2020 - 2024 (89)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (182)
	Transferases (14)
	Ligases (1)

Symmetry Type

	Asymmetric (168)
	Cyclic (18)

SCOP Classification

	Alpha and beta proteins (a/b) (76)
	Artifacts (24)
	Low resolution protein structures (1)
	Alpha and beta proteins (a+b) (5)
	All alpha proteins (3)
	All beta proteins (1)

AllSelected

1 to 25 of 182 Structures

Page 1 of 8

Sort by

Explore in 3D

1J26 \| pdb_00001j26	Download File View File

Solution structure of a putative peptidyl-tRNA hydrolase domain in a mouse hypothetical protein

Nameki, N., Kigawa, T., Koshiba, S., Kobayashi, N., Tochio, N., Inoue, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2010) J Mol Biology

Released	2004-06-01
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	immature colon carcinoma transcript 1 (protein)

Explore in 3D

1Q7S \| pdb_00001q7s	Download File View File

Crystal structure of bit1

De Pereda, J.M., Waas, W.F., Jan, Y., Ruoslahti, E., Schimmel, P., Pascual, J.

(2004) J Biological Chem 279: 8111-8115

Released	2003-12-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	bit1 (protein)

Explore in 3D

1RLK \| pdb_00001rlk	Download File View File

Structure of Conserved Protein of Unknown Function TA0108 from Thermoplasma acidophilum

Osipiuk, J., Evdokimova, E., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2003-12-30
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thermoplasma acidophilum
Macromolecule	Hypothetical protein Ta0108 (protein)
Unique Ligands	GOL, SO4

Explore in 3D

1RYB \| pdb_00001ryb	Download File View File

Crystal Structure of the Chloroplast Group II Intron Splicing Factor CRS2

Ostheimer, G.J., Barkan, A., Matthews, B.W.

(2005) J Mol Biology 345: 51-68

Released	2003-12-30
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Zea mays
Macromolecule	CRS2 (protein)

Explore in 3D

1RZW \| pdb_00001rzw	Download File View File

The Solution Structure of the Archaeglobus fulgidis protein AF2095. Northeast Structural Genomics Consortium target GR4

Powers, R., Acton, T.B., Huang, Y.J., Liu, J., Ma, L., Rost, B., Chiang, Y., Cort, J.R., Kennedy, M.A., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

(2005) Protein Sci 14: 2849-2861

Released	2004-11-16
Method	SOLUTION NMR
Organisms	Archaeoglobus fulgidus
Macromolecule	Protein AF2095(GR4) (protein)

Explore in 3D

1WN2 \| pdb_00001wn2	Download File View File

Crystal structure of project ID PH1539 from Pyrococcus horikoshii OT3

Shimizu, K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Acta Crystallogr D Biol Crystallogr 64: 444-453

Released	2005-07-19
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Peptidyl-tRNA hydrolase (protein)
Unique Ligands	NA

Explore in 3D

1XTY \| pdb_00001xty	Download File View File

Crystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase

Fromant, M., Schmitt, E., Mechulam, Y., Lazennec, C., Plateau, P., Blanquet, S.

(2005) Biochemistry 44: 4294-4301

Released	2005-03-22
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	Peptidyl-tRNA hydrolase (protein)
Unique Ligands	SO4

Explore in 3D

2D3K \| pdb_00002d3k	Download File View File

Structural study on Project ID PH1539 from Pyrococcus horikoshii OT3

Shimizu, K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Acta Crystallogr D Biol Crystallogr 64: 444-453

Released	2006-03-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Peptidyl-tRNA hydrolase (protein)
Unique Ligands	ZN

Explore in 3D

2E1B \| pdb_00002e1b	Download File View File

Crystal structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Acta Crystallogr D Biol Crystallogr 63: 390-400

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pyrococcus horikoshii
Macromolecule	216aa long hypothetical alanyl-tRNA synthetase (protein)
Unique Ligands	ZN

Explore in 3D

2JRC \| pdb_00002jrc	Download File View File

Solution structure of Peptidyl-tRNA Hydrolase from Mycobacterium tuberculosis H37Rv.

Pulavarti, S.V.S.R.K., Jain, A., Pathak, P.P., Arora, A.

(2008) J Mol Biology 378: 165-177

Released	2008-05-27
Method	SOLUTION NMR
Organisms	Mycobacterium tuberculosis
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

2LGJ \| pdb_00002lgj	Download File View File

Solution structure of MsPTH

Yadav, R., Pathak, P., Pulavarti, S., Jain, A., Kumar, A., Shukla, V., Arora, A.

To be published

Released	2012-08-01
Method	SOLUTION NMR
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

2MJL \| pdb_00002mjl	Download File View File

Solution structure of peptidyl-tRNA hyrolase from Vibrio cholerae

Kabra, A., Shahid, S., Yadav, R., Pulavarti, S., Shukla, V.K., Arora, A.

To be published

Released	2015-01-21
Method	SOLUTION NMR
Organisms	Vibrio cholerae M66-2
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

2NAF \| pdb_00002naf	Download File View File

Solution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis

Yadav, R., Pathak, P., Fatma, F., Kabra, A., Pulavarti, S., Jain, A., Kumar, A., Shukla, V., Arora, A.

(2016) Biochim Biophys Acta 1864: 1304-1314

Released	2017-01-11
Method	SOLUTION NMR
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

2PTH \| pdb_00002pth	Download File View File

PEPTIDYL-TRNA HYDROLASE FROM ESCHERICHIA COLI

Schmitt, E., Mechulam, Y., Fromant, M., Plateau, P., Blanquet, S.

(1997) EMBO J 16: 4760-4769

Released	1998-03-25
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Escherichia coli K-12
Macromolecule	PEPTIDYL-TRNA HYDROLASE (protein)

Explore in 3D

2RTX \| pdb_00002rtx	Download File View File

Solution structure of the GGQ domain of YaeJ protein from Escherichia coli

Nameki, N., Enomoto, M., Kogure, H., Tochio, N., Guntert, P.

(2014) Nucleic Acids Res 42: 3152-3163

Released	2013-12-25
Method	SOLUTION NMR
Organisms	Escherichia coli K-12
Macromolecule	Peptidyl-tRNA hydrolase YaeJ (protein)

Explore in 3D

2Z2I \| pdb_00002z2i	Download File View File

Crystal structure of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis

Selvaraj, M., Roy, S., Singh, N.S., Sangeetha, R., Varshney, U., Vijayan, M.

(2007) J Mol Biology 372: 186-193

Released	2007-07-24
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

2Z2J \| pdb_00002z2j	Download File View File

Crystal structure of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis

Selvaraj, M., Roy, S., Singh, N.S., Sangeetha, R., Varshney, U., Vijayan, M.

(2007) J Mol Biology 372: 186-193

Released	2007-07-24
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

2Z2K \| pdb_00002z2k	Download File View File

Crystal structure of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis

Selvaraj, M., Roy, S., Singh, N.S., Sangeetha, R., Varshney, U., Vijayan, M.

(2007) J Mol Biology 372: 186-193

Released	2007-07-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Peptidyl-tRNA hydrolase (protein)
Unique Ligands	CL

Explore in 3D

2ZV3 \| pdb_00002zv3	Download File View File

Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661

Shimizu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-05-05
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Methanocaldococcus jannaschii DSM 2661
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

3ERJ \| pdb_00003erj	Download File View File

Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4

Forouhar, F., Su, M., Seetharaman, J., Conover, K., Janjua, H., Xiao, R., Cunningham, K., Ma, L.-C., Cooper, B., Baran, M.C., Liu, J., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

To be published

Released	2008-10-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

3J7Y \| pdb_00003j7y	Download File View File

Structure of the large ribosomal subunit from human mitochondria

Brown, A., Amunts, A., Bai, X.C., Sugimoto, Y., Edwards, P.C., Murshudov, G., Scheres, S.H.W., Ramakrishnan, V.

(2014) Science 346: 718-722

Released	2014-10-15
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 2
Unique Ligands	AMP, MG, ZN

Explore in 3D

3J9M \| pdb_00003j9m	Download File View File

Structure of the human mitochondrial ribosome (class 1)

Amunts, A., Brown, A., Toots, J., Scheres, S.H., Ramakrishnan, V.

(2015) Science 348: 95-98

Released	2015-04-15
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 81 Unique nucleic acid chains: 4
Unique Ligands	GDP, MG, ZN

Explore in 3D

3KJZ \| pdb_00003kjz	Download File View File

Crystal structure of native peptidyl-tRNA hydrolase from Mycobacterium smegmatis

Kumar, A., Singh, N., Yadav, R., Prem Kumar, R., Sharma, S., Arora, A., Singh, T.P.

(2012) Int J Biochem Mol Biol 3: 58-69

Released	2010-08-18
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Peptidyl-tRNA hydrolase (protein)

Explore in 3D

3KK0 \| pdb_00003kk0	Download File View File

Crystal structure of partially folded intermediate state of peptidyl-tRNA hydrolase from Mycobacterium smegmatis

Kumar, A., Singh, N., Yadav, R., Sharma, S., Arora, A., Singh, T.P.

To be published

Released	2010-11-10
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Peptidyl-tRNA hydrolase (protein)
Unique Ligands	BME, EDO, IPA, PEG

Explore in 3D

3NEA \| pdb_00003nea	Download File View File

Crystal Structure of Peptidyl-tRNA hydrolase from Francisella tularensis

Lam, R., McGrath, T.E., Romanov, V., Gothe, S.A., Peddi, S.R., Razumova, E., Lipman, R.S., Branstrom, A.A., Chirgadze, N.Y.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 446-449

Released	2011-06-15
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Francisella tularensis subsp. tularensis
Macromolecule	Peptidyl-tRNA hydrolase (protein)
Unique Ligands	CL, EDO

1 to 25 of 182 Structures

Page 1 of 8

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1J26 | pdb_00001j26

1Q7S | pdb_00001q7s

1RLK | pdb_00001rlk

1RYB | pdb_00001ryb

1RZW | pdb_00001rzw

1WN2 | pdb_00001wn2

1XTY | pdb_00001xty

2D3K | pdb_00002d3k

2E1B | pdb_00002e1b

2JRC | pdb_00002jrc

2LGJ | pdb_00002lgj

2MJL | pdb_00002mjl

2NAF | pdb_00002naf

2PTH | pdb_00002pth

2RTX | pdb_00002rtx

2Z2I | pdb_00002z2i

2Z2J | pdb_00002z2j

2Z2K | pdb_00002z2k

2ZV3 | pdb_00002zv3

3ERJ | pdb_00003erj

3J7Y | pdb_00003j7y

3J9M | pdb_00003j9m

3KJZ | pdb_00003kjz

3KK0 | pdb_00003kk0

3NEA | pdb_00003nea