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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = Y1

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Wolinella succinogenes (7)
	Escherichia coli (3)
	Human immunodeficiency virus type 1 BH10 (3)
	Alcaligenes faecalis (1)
	Calloselasma rhodostoma (1)
	Helicoverpa zea (1)
	Homo sapiens (1)
	Human immunodeficiency virus 1 (1)
	Moorella thermoacetica (1)
	Salmonella enterica subsp. enterica serovar Typhimurium (1)

Taxonomy

	Bacteria (13)
	Riboviria (4)
	Eukaryota (2)

Experimental Method

X-RAY DIFFRACTION (19)

Polymer Entity Type

Protein (19)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (8)
	2.0 - 2.5 (6)
	3.0 - 3.5 (1)

Release Date

	2000 - 2004 (6)
	2005 - 2009 (8)
	2010 - 2014 (1)
	2015 - 2019 (4)

Enzyme Classification Name

	Oxidoreductases (7)
	Hydrolases (4)
	Transferases (1)
	Isomerases (1)

Symmetry Type

	Asymmetric (8)
	Cyclic (11)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (3)
	All alpha proteins (10)
	All beta proteins (5)
	Alpha and beta proteins (a/b) (2)
	Artifacts (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 19 of 19 Structures

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1DDE \| pdb_00001dde	Download File View File

STRUCTURE OF THE DNAG CATALYTIC CORE

Keck, J.L., Roche, D.D., Lynch, A.S., Berger, J.M.

(2000) Science 287: 2482-2486

Released	2000-04-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	DNA PRIMASE (protein)
Unique Ligands	Y1

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1FS7 \| pdb_00001fs7	Download File View File

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES

Einsle, O., Stach, P., Messerschmidt, A., Simon, J., Kroeger, A., Huber, R., Kroneck, P.M.H.

(2000) J Biological Chem 275: 39608-39616

Released	2001-01-17
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Wolinella succinogenes
Macromolecule	CYTOCHROME C NITRITE REDUCTASE (protein)
Unique Ligands	ACT, CA, HEC, Y1

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1FS8 \| pdb_00001fs8	Download File View File

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES-SULFATE COMPLEX

Einsle, O., Stach, P., Messerschmidt, A., Simon, J., Kroeger, A., Huber, R., Kroneck, P.M.H.

(2000) J Biological Chem 275: 39608-39616

Released	2001-01-17
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Wolinella succinogenes
Macromolecule	CYTOCHROME C NITRITE REDUCTASE (protein)
Unique Ligands	ACT, CA, HEC, SO4, Y1

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1FS9 \| pdb_00001fs9	Download File View File

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES-AZIDE COMPLEX

Einsle, O., Stach, P., Messerschmidt, A., Simon, J., Kroeger, A., Huber, R., Kroneck, P.M.H.

(2000) J Biological Chem 275: 39608-39616

Released	2001-01-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Wolinella succinogenes
Macromolecule	CYTOCHROME C NITRITE REDUCTASE (protein)
Unique Ligands	AZI, CA, HEC, Y1

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1LVA \| pdb_00001lva	Download File View File

Crystal structure of a C-terminal fragment of Moorella thermoacetica elongation factor SelB

Selmer, M., Su, X.-D.

(2002) EMBO J 21: 4145-4153

Released	2002-08-21
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Moorella thermoacetica
Macromolecule	Selenocysteine-specific elongation factor (protein)
Unique Ligands	SO4, Y1

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1PY0 \| pdb_00001py0	Download File View File

Crystal structure of E51C/E54C Psaz from A.faecalis with CLaNP probe

Prudencio, M., Rohovec, J., Peters, J.A., Tocheva, E., Boulanger, M.J., Murphy, M.E., Hupkes, H.J., Kosters, W., Impagliazzo, A., Ubbink, M.

(2004) Chemistry 10: 3252-3260

Released	2004-12-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Alcaligenes faecalis
Macromolecule	Pseudoazurin (protein)
Unique Ligands	SO4, Y1, YMA, ZN

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1R6O \| pdb_00001r6o	Download File View File

ATP-dependent Clp protease ATP-binding subunit clpA/ATP-dependent Clp protease adaptor protein clpS

Xia, D., Maurizi, M.R., Guo, F., Singh, S.K., Esser, L.

(2004) J Struct Biol 146: 166-179

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Escherichia coli
Macromolecule	ATP-dependent Clp protease ATP-binding subunit clpA (protein) ATP-dependent Clp protease adaptor protein clpS (protein)
Unique Ligands	CL, GOL, Y1, YBT, ZN

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1R6Q \| pdb_00001r6q	Download File View File

ClpNS with fragments

Xia, D., Maurizi, M.R., Guo, F., Singh, S.K., Esser, L.

(2004) J Struct Biol 146: 166-179

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Escherichia coli
Macromolecule	ATP-dependent Clp protease ATP-binding subunit clpA (protein) ATP-dependent Clp protease adaptor protein clpS (protein)
Unique Ligands	GOL, Y1, YBT

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2C1C \| pdb_00002c1c	Download File View File

Structural basis of the resistance of an insect carboxypeptidase to plant protease inhibitors

Bayes, A., Comellas-Bigler, M., Rodriguez de la Vega, M., Maskos, K., Bode, W., Aviles, F.X., Jongsma, M.A., Beekwilder, J., Vendrell, J.

(2005) Proc Natl Acad Sci U S A 102: 16602

Released	2005-10-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Helicoverpa zea
Macromolecule	CARBOXYPEPTIDASE B (protein)
Unique Ligands	Y1, ZN

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3BNF \| pdb_00003bnf	Download File View File

W. succinogenes NrfA Sulfite Complex

Lukat, P., Einsle, O.

(2008) Biochemistry 47: 2080-2086

Released	2008-02-26
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Wolinella succinogenes
Macromolecule	Cytochrome c-552 (protein)
Unique Ligands	ACT, CA, HEM, SO3, Y1

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3BNG \| pdb_00003bng	Download File View File

W. succinogenes NrfA Y218F

Lukat, P., Einsle, O.

(2008) Biochemistry 47: 2080-2086

Released	2008-02-26
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Wolinella succinogenes
Macromolecule	Cytochrome c-552 (protein)
Unique Ligands	ACT, CA, HEM, SO4, Y1

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3BNH \| pdb_00003bnh	Download File View File

W. succinogenes NrfA Y218F Nitrite Complex

Lukat, P., Einsle, O.

(2008) Biochemistry 47: 2080-2086

Released	2008-02-26
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Wolinella succinogenes
Macromolecule	Cytochrome c-552 (protein)
Unique Ligands	ACT, CA, HEM, NO2, SO4, Y1

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3BNJ \| pdb_00003bnj	Download File View File

W. succinogenes NrfA Y218F Sulfite Complex

Lukat, P., Einsle, O.

(2008) Biochemistry 47: 2080-2086

Released	2008-02-26
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Wolinella succinogenes
Macromolecule	Cytochrome c-552 (protein)
Unique Ligands	ACT, CA, HEM, SO3, SO4, Y1

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3H1W \| pdb_00003h1w	Download File View File

Crystal structure of mannose 6-phosphate isomerase bound with zinc and yttrium

Sagurthi, S.R., Giri, G., Savithri, H.S., Murthy, M.R.N.

To be published

Released	2009-05-19
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Mannose-6-phosphate isomerase (protein)
Unique Ligands	EDO, Y1, ZN

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3UF3 \| pdb_00003uf3	Download File View File

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical isolate PR20

Agniswamy, J., Chen-Hsiang, S., Aniana, A., Sayer, J.M., Louis, J.M., Weber, I.T.

(2012) Biochemistry 51: 2819-2828

Released	2012-03-28
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	HIV-1 protease (protein)
Unique Ligands	GOL, Y1

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4YE3 \| pdb_00004ye3	Download File View File

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 with Inhibitor GRL-4410A

Agniswamy, J., Weber, I.T.

(2015) J Med Chem 58: 5088-5095

Released	2015-06-10
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Human immunodeficiency virus type 1 BH10
Macromolecule	Protease (protein)
Unique Ligands	CL, G04, GOL, Y1

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4YHQ \| pdb_00004yhq	Download File View File

Crystal structure of multidrug resistant clinical isolate PR20 with GRL-5010A

Agniswamy, J., Weber, I.T.

(2015) J Med Chem 58: 5088-5095

Released	2015-06-10
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Human immunodeficiency virus type 1 BH10
Macromolecule	Protease (protein)
Unique Ligands	CL, G10, GOL, NA, Y1

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6NDG \| pdb_00006ndg	Download File View File

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH YTTRIUM BOUND

Stetefeld, J., McDougall, M.D., Loewen, P.C.

To be published

Released	2019-01-23
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Calloselasma rhodostoma Homo sapiens
Macromolecule	Integrin alpha-2 (protein) Snaclec rhodocetin subunit delta (protein) Snaclec rhodocetin subunit gamma (protein)
Unique Ligands	CL, NA, NH4, SO4, Y1

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6PRF \| pdb_00006prf	Download File View File

HIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A

Kneller, D.W., Agniswamy, J., Weber, I.T.

(2019) Biochem Biophys Res Commun 519: 61-66

Released	2019-09-18
Method	X-RAY DIFFRACTION 1.21 Å
Organisms	Human immunodeficiency virus type 1 BH10
Macromolecule	Protease (protein)
Unique Ligands	7OA, Y1

1 to 19 of 19 Structures

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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.

1DDE | pdb_00001dde

STRUCTURE OF THE DNAG CATALYTIC CORE

1FS7 | pdb_00001fs7

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES

1FS8 | pdb_00001fs8

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES-SULFATE COMPLEX

1FS9 | pdb_00001fs9

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES-AZIDE COMPLEX

1LVA | pdb_00001lva

Crystal structure of a C-terminal fragment of Moorella thermoacetica elongation factor SelB

1PY0 | pdb_00001py0

Crystal structure of E51C/E54C Psaz from A.faecalis with CLaNP probe

1R6O | pdb_00001r6o

ATP-dependent Clp protease ATP-binding subunit clpA/ATP-dependent Clp protease adaptor protein clpS

1R6Q | pdb_00001r6q

ClpNS with fragments

2C1C | pdb_00002c1c

Structural basis of the resistance of an insect carboxypeptidase to plant protease inhibitors

3BNF | pdb_00003bnf

W. succinogenes NrfA Sulfite Complex

3BNG | pdb_00003bng

W. succinogenes NrfA Y218F

3BNH | pdb_00003bnh

W. succinogenes NrfA Y218F Nitrite Complex

3BNJ | pdb_00003bnj

W. succinogenes NrfA Y218F Sulfite Complex

3H1W | pdb_00003h1w

Crystal structure of mannose 6-phosphate isomerase bound with zinc and yttrium

3UF3 | pdb_00003uf3

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical isolate PR20

4YE3 | pdb_00004ye3

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 with Inhibitor GRL-4410A

4YHQ | pdb_00004yhq

Crystal structure of multidrug resistant clinical isolate PR20 with GRL-5010A

6NDG | pdb_00006ndg

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH YTTRIUM BOUND

6PRF | pdb_00006prf

HIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A

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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

1DDE | pdb_00001dde

1FS7 | pdb_00001fs7

1FS8 | pdb_00001fs8

1FS9 | pdb_00001fs9

1LVA | pdb_00001lva

1PY0 | pdb_00001py0

1R6O | pdb_00001r6o

1R6Q | pdb_00001r6q

2C1C | pdb_00002c1c

3BNF | pdb_00003bnf

3BNG | pdb_00003bng

3BNH | pdb_00003bnh

3BNJ | pdb_00003bnj

3H1W | pdb_00003h1w

3UF3 | pdb_00003uf3

4YE3 | pdb_00004ye3

4YHQ | pdb_00004yhq

6NDG | pdb_00006ndg

6PRF | pdb_00006prf