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: Structure Author = "Yu, X."

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 280 Structures.

Refinements

Structure Determination Methodology

experimental (280)

Scientific Name of Source Organism

	Homo sapiens (127)
	Mus musculus (24)
	synthetic construct (24)
	Escherichia coli (13)
	Severe acute respiratory syndrome coronavirus 2 (10)
	Xanthomonas campestris pv. campestris str. ATCC 33913 (9)
	Human betaherpesvirus 5 (8)
	Mycobacterium tuberculosis H37Rv (7)
	Enterococcus faecalis (6)
	Lama glama (6)

More...

Taxonomy

	Eukaryota (153)
	Bacteria (79)
	Riboviria (40)
	other sequences (24)
	Duplodnaviria (15)
	Monodnaviria (7)
	Varidnaviria (3)
	Adnaviria (2)
	Archaea (2)

Experimental Method

	ELECTRON MICROSCOPY (145)
	X-RAY DIFFRACTION (134)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (280)
	RNA (9)
	DNA (6)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (38)
	2.0 - 2.5 (48)
	2.5 - 3.0 (64)
	3.0 - 3.5 (58)
	3.5 - 4.0 (31)
	4.0 - 4.5 (20)
	> 4.5 (17)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (9)
	2005 - 2009 (22)
	2010 - 2014 (46)
	2015 - 2019 (61)
	2020 - 2024 (133)
	2025 - 2029 (8)

Enzyme Classification Name

	Hydrolases (82)
	Transferases (63)
	Lyases (6)
	Oxidoreductases (8)
	Ligases (3)
	Translocases (1)
	Isomerases (1)

Membrane Protein Annotation

	PDBTM (52)
	OPM (49)
	mpstruc (38)
	MemProtMD (31)

Symmetry Type

	Asymmetric (158)
	Cyclic (89)
	Dihedral (17)
	Helical (13)
	Icosahedral (9)

SCOP Classification

	All beta proteins (26)
	Alpha and beta proteins (a/b) (34)
	Alpha and beta proteins (a+b) (20)
	Artifacts (9)
	Low resolution protein structures (2)
	All alpha proteins (7)
	Multi-domain proteins (alpha and beta) (4)
	Coiled coil proteins (1)

AllSelected

1 to 25 of 280 Structures

Page 1 of 12

Sort by

Explore in 3D

1C9Y \| pdb_00001c9y	Download File View File

HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM

Shi, D., Yu, X., Morizono, H., Tuchman, M., Allewell, N.M.

(2000) Proteins 39: 271-277

Released	2000-06-06
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	ORNITHINE CARBAMOYLTRANSFERASE (protein)
Unique Ligands	CP, NVA

Explore in 3D

1EP9 \| pdb_00001ep9	Download File View File

HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE

Shi, D., Morizono, H., Yu, X., Allewell, N.M., Tuchman, M.

(2001) Biochem J 354: 501-509

Released	2001-04-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	ORNITHINE TRANSCARBAMYLASE (protein)
Unique Ligands	CP

Explore in 3D

1FVO \| pdb_00001fvo	Download File View File

CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE

Shi, D., Morizono, H., Yu, X., Allewell, N.M., Tuchman, M.

(2001) Biochem J 354: 501-509

Released	2001-04-04
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	ORNITHINE TRANSCARBAMYLASE (protein)
Unique Ligands	CP

Explore in 3D

1JS1 \| pdb_00001js1	Download File View File

Crystal Structure of a new transcarbamylase from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution

Shi, D., Gallegos, R., DePonte III, J., Morizono, H., Yu, X., Allewell, N.M., Malamy, M., Tuchman, M.

(2002) J Mol Biology 320: 899-908

Released	2002-07-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bacteroides fragilis
Macromolecule	Transcarbamylase (protein)
Unique Ligands	PO4

Explore in 3D

1N03 \| pdb_00001n03	Download File View File

Model for Active RecA Filament

VanLoock, M.S., Yu, X., Yang, S., Lai, A.L., Low, C., Campbell, M.J., Egelman, E.H.

(2003) Structure 11: 187-196

Released	2003-02-25
Method	ELECTRON MICROSCOPY 20 Å
Organisms	Escherichia coli
Macromolecule	RecA protein (protein)
Unique Ligands	ADP

Explore in 3D

1OS5 \| pdb_00001os5	Download File View File

Crystal structure of HCV NS5B RNA polymerase complexed with a novel non-competitive inhibitor.

Love, R.A., Parge, H.E., Yu, X., Hickey, M.J., Diehl, W., Gao, J., Wriggers, H., Ekker, A., Wang, L., Thomson, J.A., Dragovich, P.S., Fuhrman, S.A.

(2003) J Virol 77: 7575-7581

Released	2004-03-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hepatitis C virus subtype 1b
Macromolecule	Hepatitis C virus NS5B RNA polymerase (protein)
Unique Ligands	NH1

Explore in 3D

1WT9 \| pdb_00001wt9	Download File View File

crystal structure of Aa-X-bp-I, a snake venom protein with the activity of binding to coagulation factor X from Agkistrodon acutus

Zhu, Z., Liu, S., Mo, X., Yu, X., Liang, Z., Zang, J., Zhao, W., Teng, M., Niu, L.

To be published

Released	2006-03-07
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Deinagkistrodon acutus
Macromolecule	agkisacutacin A chain (protein) anticoagulant protein-B (protein)
Unique Ligands	CA

Explore in 3D

1XR5 \| pdb_00001xr5	Download File View File

Crystal Structure of the RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 14

Love, R.A., Maegley, K.A., Yu, X., Ferre, R.A., Lingardo, L.K., Diehl, W., Parge, H.E., Dragovich, P.S., Fuhrman, S.A.

(2004) Structure 12: 1533-1544

Released	2004-10-26
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	rhinovirus B14
Macromolecule	Genome polyprotein (protein)
Unique Ligands	SM

Explore in 3D

1XR6 \| pdb_00001xr6	Download File View File

Crystal Structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 1B

Love, R.A., Maegley, K.A., Yu, X., Ferre, R.A., Lingardo, L.K., Diehl, W., Parge, H.E., Dragovich, P.S., Fuhrman, S.A.

(2004) Structure 12: 1533-1544

Released	2004-10-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	rhinovirus A1B
Macromolecule	Genome polyprotein (protein)
Unique Ligands	K

Explore in 3D

1XR7 \| pdb_00001xr7	Download File View File

Crystal structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 16

Love, R.A., Maegley, K.A., Yu, X., Ferre, R.A., Lingardo, L.K., Diehl, W., Parge, H.E., Dragovich, P.S., Fuhrman, S.A.

(2004) Structure 12: 1533-1544

Released	2004-10-26
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	rhinovirus A16
Macromolecule	Genome polyprotein (protein)

Explore in 3D

1Y17 \| pdb_00001y17	Download File View File

crystal structure of Aa-X-bp-II, a snake venom protein with the activity of binding to coagulation factor X from Agkistrodon acutus

Zhu, Z., Liu, S., Mo, X., Yu, X., Liang, Z., Zang, J., Zhao, W., Teng, M., Niu, L.

To be published

Released	2006-03-07
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Deinagkistrodon acutus
Macromolecule	anticoagulant protein A (protein) anticoagulant protein-B (protein)
Unique Ligands	CA

Explore in 3D

2F7V \| pdb_00002f7v	Download File View File

Structure of acetylcitrulline deacetylase complexed with one Co

Shi, D., Yu, X., Roth, L., Allewell, N.M., Tuchman, M.

(2007) Biophys Chem 126: 86-93

Released	2006-09-26
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Xanthomonas campestris
Macromolecule	aectylcitrulline deacetylase (protein)
Unique Ligands	CO

Explore in 3D

2F8H \| pdb_00002f8h	Download File View File

Structure of acetylcitrulline deacetylase from Xanthomonas campestris in metal-free form

Shi, D., Yu, X., Roth, L., Allewell, N.M., Tuchman, M.

(2007) Biophys Chem 126: 86-93

Released	2006-09-26
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Xanthomonas campestris
Macromolecule	aectylcitrulline deacetylase (protein)

Explore in 3D

2FG6 \| pdb_00002fg6	Download File View File

N-succinyl-L-ornithine transcarbamylase from B. fragilis complexed with sulfate and N-succinyl-L-norvaline

Shi, D., Yu, X., Malamy, M.H., Allewell, N.M., Mendel, T.

(2006) J Biological Chem 281: 20623-20631

Released	2006-05-23
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bacteroides fragilis NCTC 9343
Macromolecule	putative ornithine carbamoyltransferase (protein)
Unique Ligands	SN0, SO4

Explore in 3D

2FG7 \| pdb_00002fg7	Download File View File

N-succinyl-L-ornithine transcarbamylase from B. fragilis complexed with carbamoyl phosphate and N-succinyl-L-norvaline

Shi, D., Yu, X., Malamy, M.H., Allewell, N.M., Tuchman, M.

(2006) J Biological Chem 281: 20623-20631

Released	2006-05-23
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Bacteroides fragilis NCTC 9343
Macromolecule	putative ornithine carbamoyltransferase (protein)
Unique Ligands	CP, SN0, SO4

Explore in 3D

2G7M \| pdb_00002g7m	Download File View File

Crystal structure of B. fragilis N-succinylornithine transcarbamylase P90E mutant complexed with carbamoyl phosphate and N-acetylnorvaline

Shi, D., Yu, X., Roth, L., Morizono, H., Allewell, N.M., Tuchman, M.

(2007) Protein Sci 16: 1689-1699

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Bacteroides fragilis
Macromolecule	putative ornithine carbamoyltransferase (protein)
Unique Ligands	AN0, CP, SO4

Explore in 3D

2HI5 \| pdb_00002hi5	Download File View File

Model for bacteriophage fd from cryo-EM

Wang, Y.A., Yu, X., Overman, S., Tsuboi, M., Thomas, G.J., Egelman, E.H.

(2006) J Mol Biology 361: 209-215

Released	2007-08-07
Method	ELECTRON MICROSCOPY 8 Å
Organisms	Enterobacteria phage fd
Macromolecule	Coat protein B (protein)

Explore in 3D

2QCJ \| pdb_00002qcj	Download File View File

Native Structure of Lyp

Sun, J.P., Yu, X., Zhang, Z.Y.

To be published

Released	2007-11-20
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein phosphatase non-receptor type 22 (protein)

Explore in 3D

2QCT \| pdb_00002qct	Download File View File

Structure of Lyp with inhibitor I-C11

Yu, X., Sun, J.P., Zhang, Z.Y.

To be published

Released	2007-11-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein phosphatase non-receptor type 22 (protein)
Unique Ligands	561, EDO

Explore in 3D

2R8V \| pdb_00002r8v	Download File View File

Native structure of N-acetylglutamate synthase from Neisseria gonorrhoeae

Shi, D., Sagar, V., Jin, Z., Yu, X., Caldovic, L., Morizono, H., Allewell, N.M., Tuchman, M.

(2008) J Biological Chem 283: 7176-7184

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Neisseria gonorrhoeae
Macromolecule	Putative acetylglutamate synthase (protein)
Unique Ligands	ACO

Explore in 3D

2R98 \| pdb_00002r98	Download File View File

Crystal Structure of N-acetylglutamate synthase (selenoMet substituted) from Neisseria gonorrhoeae

Shi, D., Sagar, V., Jin, Z., Yu, X., Caldovic, L., Morizono, H., Allewell, N.M., Tuchman, M.

(2008) J Biological Chem 283: 7176-7184

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Neisseria gonorrhoeae
Macromolecule	Putative acetylglutamate synthase (protein)
Unique Ligands	ACO

Explore in 3D

2REC \| pdb_00002rec	Download File View File

RECA HEXAMER MODEL, ELECTRON MICROSCOPY

Yu, X., Egelman, E.H.

(1997) Nat Struct Biol 4: 101-104

Released	1997-04-01
Method	ELECTRON MICROSCOPY
Organisms	Escherichia coli
Macromolecule	RECA (protein)

Explore in 3D

3B8G \| pdb_00003b8g	Download File View File

Crysta structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and N-acetyl-glutamate

Shi, D., Sagar, V., Jin, Z., Yu, X., Caldovic, L., Morizono, H., Allewell, N.M., Tuchman, M.

(2008) J Biological Chem 283: 7176-7184

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Neisseria gonorrhoeae
Macromolecule	Putative acetylglutamate synthase (protein)
Unique Ligands	COA, NLG