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 = "Xu, 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 505 Structures.

Refinements

Structure Determination Methodology

experimental (505)

Scientific Name of Source Organism

	Homo sapiens (69)
	Agrobacterium fabrum str. C58 (48)
	Chloroflexus aurantiacus J-10-fl (24)
	Streptomyces coelicolor A3(2) (18)
	Aquifex aeolicus (15)
	Saccharomyces cerevisiae (13)
	Pseudomonas aeruginosa (11)
	synthetic construct (11)
	Escherichia coli (9)
	Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (9)

More...

Taxonomy

	Bacteria (324)
	Eukaryota (119)
	Riboviria (35)
	Archaea (26)
	other sequences (11)
	Duplodnaviria (8)
	unclassified sequences (7)
	Riboviria (RNA viruses and viroids) (2)

Experimental Method

	X-RAY DIFFRACTION (422)
	ELECTRON MICROSCOPY (70)
	SOLUTION NMR (13)

Polymer Entity Type

	Protein (505)
	RNA (9)
	DNA (8)

Refinement Resolution (Å)

	1.0 - 1.5 (35)
	1.5 - 2.0 (175)
	2.0 - 2.5 (139)
	2.5 - 3.0 (63)
	3.0 - 3.5 (47)
	3.5 - 4.0 (17)
	4.0 - 4.5 (8)
	> 4.5 (8)

Release Date

	1995 - 1999 (3)
	2000 - 2004 (27)
	2005 - 2009 (184)
	2010 - 2014 (111)
	2015 - 2019 (61)
	2020 - 2024 (98)
	2025 - 2029 (21)

Enzyme Classification Name

	Hydrolases (104)
	Transferases (51)
	Oxidoreductases (10)
	Translocases (8)
	Lyases (11)
	Ligases (8)
	Isomerases (5)

Membrane Protein Annotation

	PDBTM (36)
	MemProtMD (22)
	mpstruc (21)
	OPM (10)

Symmetry Type

	Asymmetric (247)
	Cyclic (239)
	Dihedral (51)
	Icosahedral (2)
	Tetrahedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (83)
	Alpha and beta proteins (a+b) (51)
	Artifacts (58)
	All beta proteins (37)
	All alpha proteins (34)
	Small proteins (3)
	Membrane and cell surface proteins and peptides (2)
	Multi-domain proteins (alpha and beta) (1)
	Peptides (1)

AllSelected

1 to 25 of 505 Structures

Page 1 of 21

Sort by

Explore in 3D

1ALH \| pdb_00001alh	Download File View File

KINETICS AND CRYSTAL STRUCTURE OF A MUTANT E. COLI ALKALINE PHOSPHATASE (ASP-369-->ASN): A MECHANISM INVOLVING ONE ZINC PER ACTIVE SITE

Tibbitts, T.T., Xu, X., Kantrowitz, E.R.

(1994) Protein Sci 3: 2005-2014

Released	1995-02-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	ALKALINE PHOSPHATASE (protein)
Unique Ligands	PO4, SO4, ZN

Explore in 3D

1BLX \| pdb_00001blx	Download File View File

P19INK4D/CDK6 COMPLEX

Brotherton, D.H., Dhanaraj, V., Wick, S., Brizuela, L., Domaille, P.J., Volyanik, E., Xu, X., Parisini, E., Smith, B.O., Archer, S.J., Serrano, M., Brenner, S.L., Blundell, T.L., Laue, E.D.

(1998) Nature 395: 244-250

Released	1999-06-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	CYCLIN-DEPENDENT KINASE 6 (protein) P19INK4D (protein)
Unique Ligands	CA

Explore in 3D

1KYT \| pdb_00001kyt	Download File View File

Crystal Structure of Thermoplasma acidophilum 0175 (APC014)

Kim, Y., Joachimiak, A., Edwards, A., Xu, X., Pennycooke, M., Gu, J., Cheung, F., Christendat, D., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2003-01-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermoplasma acidophilum
Macromolecule	hypothetical protein TA0175 (protein)
Unique Ligands	CA

Explore in 3D

1L1S \| pdb_00001l1s	Download File View File

Structure of Protein of Unknown Function MTH1491 from Methanobacterium thermoautotrophicum

Christendat, D., Saridakis, V., Kim, Y., Kumar, P.A., Xu, X., Semesi, A., Joachimiak, A., Arrowsmith, C.H., Edwards, A.M., Midwest Center for Structural Genomics (MCSG)

(2002) Protein Sci 11: 1409-1414

Released	2002-05-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanothermobacter thermautotrophicus
Macromolecule	hypothetical protein MTH1491 (protein)

Explore in 3D

1L6R \| pdb_00001l6r	Download File View File

Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)

Kim, Y., Joachimiak, A., Edwards, A.M., Xu, X., Pennycooke, M., Gu, J., Cheung, F., Christendat, D., Midwest Center for Structural Genomics (MCSG)

(2004) J Biological Chem 279: 517-526

Released	2003-01-21
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Thermoplasma acidophilum
Macromolecule	HYPOTHETICAL PROTEIN TA0175 (protein)
Unique Ligands	CA, FMT

Explore in 3D

1LXJ \| pdb_00001lxj	Download File View File

X-RAY STRUCTURE OF YBL001c NORTHEAST STRUCTURAL GENOMICS (NESG) CONSORTIUM TARGET YTYst72

Tao, X., Khayat, R., Christendat, D., Savchenko, A., Xu, X., Edwards, A., Arrowsmith, C.H., Tong, L., Northeast Structural Genomics Consortium (NESG)

(2003) Proteins 52: 478-480

Released	2003-07-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION (protein)
Unique Ligands	SO4

Explore in 3D

1LXN \| pdb_00001lxn	Download File View File

X-RAY STRUCTURE OF MTH1187 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TT272

Tao, X., Khayat, R., Christendat, D., Savchenko, A., Xu, X., Edwards, A., Arrowsmith, C.H., Tong, L., Northeast Structural Genomics Consortium (NESG)

(2003) Proteins 52: 478-480

Released	2003-07-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanothermobacter thermautotrophicus
Macromolecule	HYPOTHETICAL PROTEIN MTH1187 (protein)
Unique Ligands	SO4

Explore in 3D

1NE2 \| pdb_00001ne2	Download File View File

Crystal Structure of Thermoplasma acidophilum 1320 (APC5513)

Kim, Y., Joachimiak, A., Edwards, A., Xu, X., Christendat, D., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2003-07-01
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Thermoplasma acidophilum
Macromolecule	hypothetical protein ta1320 (protein)
Unique Ligands	FMT

Explore in 3D

1NJK \| pdb_00001njk	Download File View File

Crystal Structure of YbaW Probable Thioesterase from Escherichia coli

Kim, Y., Joachimiak, A., Edwards, A., Xu, X., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2003-07-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	Hypothetical protein ybaW (protein)
Unique Ligands	IOD

Explore in 3D

1NOG \| pdb_00001nog	Download File View File

Crystal Structure of Conserved Protein 0546 from Thermoplasma Acidophilum

Saridakis, V., Sanishvili, R., Iakounine, A., Xu, X., Pennycooke, M., Gu, J., Joachimiak, A., Arrowsmith, C.H., Edwards, A.M., Christendat, D., Midwest Center for Structural Genomics (MCSG)

(2004) J Biological Chem 279: 23646-23653

Released	2003-07-29
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Thermoplasma acidophilum
Macromolecule	conserved hypothetical protein TA0546 (protein)

Explore in 3D

1O5T \| pdb_00001o5t	Download File View File

Crystal structure of the aminoacylation catalytic fragment of human tryptophanyl-tRNA synthetase

Yu, Y., Liu, Y., Shen, N., Xu, X., Jia, J., Jin, Y., Arnold, E., Ding, J.

(2004) J Biological Chem 279: 8378-8388

Released	2004-07-06
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Tryptophanyl-tRNA synthetase (protein)

Explore in 3D

1P8C \| pdb_00001p8c	Download File View File

Crystal structure of TM1620 (APC4843) from Thermotoga maritima

Kim, Y., Joachimiak, A., Brunzelle, J.S., Korolev, S.V., Edwards, A., Xu, X., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2003-09-23
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermotoga maritima
Macromolecule	conserved hypothetical protein (protein)

Explore in 3D

1PCK \| pdb_00001pck	Download File View File

Aquifex aeolicus KDO8PS in complex with Z-methyl-PEP

Wang, J., Xu, X., Grison, C., Petek, S., Coutrot, P., Birck, M., Woodard, R.W., Gatti, D.L.

(2003) Drug Des Discov 18: 91-99

Released	2004-02-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aquifex aeolicus
Macromolecule	2-dehydro-3-deoxyphosphooctonate aldolase (protein)
Unique Ligands	CD, PEZ, PO4

Explore in 3D

1PCW \| pdb_00001pcw	Download File View File

Aquifex aeolicus KDO8PS in complex with cadmium and APP, a bisubstrate inhibitor

Xu, X., Wang, J., Grison, C., Petek, S., Coutrot, P., Birck, M., Woodard, R.W., Gatti, D.L.

(2003) Drug Des Discov 18: 91-99

Released	2004-02-17
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Aquifex aeolicus
Macromolecule	2-dehydro-3-deoxyphosphooctonate aldolase (protein)
Unique Ligands	CD, H4P

Explore in 3D

1PE1 \| pdb_00001pe1	Download File View File

Aquifex aeolicus KDO8PS in complex with cadmium and 2-PGA

Wang, J., Xu, X., Grison, C., Petek, S., Coutrot, P., Birck, M.R., Woodard, R.W., Gatti, D.L.

(2003) Drug Des Discov 18: 91-99

Released	2004-02-03
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Aquifex aeolicus
Macromolecule	2-dehydro-3-deoxyphosphooctonate aldolase (protein)
Unique Ligands	2PG, CD, PO4

Explore in 3D

1Q7H \| pdb_00001q7h	Download File View File

Structure of a Conserved PUA Domain Protein from Thermoplasma acidophilum

Cuff, M.E., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2004-01-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermoplasma acidophilum DSM 1728
Macromolecule	conserved hypothetical protein (protein)
Unique Ligands	ZN

Explore in 3D

1R0U \| pdb_00001r0u	Download File View File

Crystal structure of ywiB protein from Bacillus subtilis

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

To be published

Released	2003-12-30
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Bacillus subtilis
Macromolecule	protein ywiB (protein)
Unique Ligands	GOL

Explore in 3D

1RLH \| pdb_00001rlh	Download File View File

Structure of a conserved protein from Thermoplasma acidophilum

Cuff, M.E., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2004-05-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermoplasma acidophilum
Macromolecule	conserved hypothetical protein (protein)
Unique Ligands	NA

Explore in 3D

1T09 \| pdb_00001t09	Download File View File

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex NADP

Xu, X., Zhao, J., Peng, B., Huang, Q., Arnold, E., Ding, J.

(2004) J Biological Chem 279: 33946-33957

Released	2004-06-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Isocitrate dehydrogenase [NADP] cytoplasmic (protein)
Unique Ligands	NAP

Explore in 3D

1T0L \| pdb_00001t0l	Download File View File

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+)

Xu, X., Zhao, J., Peng, B., Huang, Q., Arnold, E., Ding, J.

(2004) J Biological Chem 279: 33946-33957

Released	2004-06-15
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Homo sapiens
Macromolecule	Isocitrate dehydrogenase [NADP] cytoplasmic (protein)
Unique Ligands	CA, ICT, NAP

Explore in 3D

1T1J \| pdb_00001t1j	Download File View File

Crystal structure of genomics APC5043

Dong, A., Xu, X., Liu, Y., Zhang, R., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2004-08-03
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	hypothetical protein (protein)

Explore in 3D

1T57 \| pdb_00001t57	Download File View File

Crystal Structure of the Conserved Protein MTH1675 from Methanobacterium thermoautotrophicum

Kim, Y., Joachimiak, A., Saridakis, V., Xu, X., Arrowsmith, C.H., Christendat, D., Edwards, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2004-08-03
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanothermobacter thermautotrophicus
Macromolecule	Conserved Protein MTH1675 (protein)
Unique Ligands	FMN, MG