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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Li, D."

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Search Summary

This query matches 284 Structures.

Refinements

Structure Determination Methodology

experimental (284)

Scientific Name of Source Organism

	Homo sapiens (171)
	synthetic construct (30)
	Escherichia coli K-12 (15)
	Mycobacterium tuberculosis (10)
	Severe acute respiratory syndrome coronavirus 2 (10)
	Monkeypox virus (9)
	Mus musculus (8)
	Aquifex aeolicus VF5 (5)
	Cyclocybe aegerita (5)
	DNA molecule (4)

More...

Taxonomy

	Eukaryota (203)
	Bacteria (60)
	other sequences (30)
	Riboviria (19)
	Varidnaviria (10)
	unclassified sequences (4)
	Duplodnaviria (2)
	Eukaryota (eukaryotes) (2)
	Archaea (1)
	Monodnaviria (1)

Experimental Method

	ELECTRON MICROSCOPY (144)
	X-RAY DIFFRACTION (129)
	ELECTRON CRYSTALLOGRAPHY (6)
	SOLUTION NMR (5)

Polymer Entity Type

	Protein (284)
	DNA (6)
	RNA (5)

Refinement Resolution (Å)

	0.5 - 1.0 (7)
	1.0 - 1.5 (11)
	1.5 - 2.0 (29)
	2.0 - 2.5 (56)
	2.5 - 3.0 (85)
	3.0 - 3.5 (68)
	3.5 - 4.0 (21)
	4.0 - 4.5 (1)
	> 4.5 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (9)
	2005 - 2009 (9)
	2010 - 2014 (34)
	2015 - 2019 (40)
	2020 - 2024 (180)
	2025 - 2029 (11)

Enzyme Classification Name

	Hydrolases (41)
	Transferases (39)
	Isomerases (6)
	Oxidoreductases (6)
	Lyases (3)

Membrane Protein Annotation

	MemProtMD (35)
	PDBTM (39)
	OPM (17)
	mpstruc (15)

Symmetry Type

	Asymmetric (138)
	Cyclic (80)
	Helical (53)
	Dihedral (17)

SCOP Classification

	Alpha and beta proteins (a+b) (18)
	Membrane and cell surface proteins and peptides (12)
	Artifacts (9)
	All beta proteins (7)
	Alpha and beta proteins (a/b) (9)
	All alpha proteins (6)
	Small proteins (5)

AllSelected

1 to 25 of 284 Structures

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1CUN \| pdb_00001cun	Download File View File

CRYSTAL STRUCTURE OF REPEATS 16 AND 17 OF CHICKEN BRAIN ALPHA SPECTRIN

Grum, V.L., Li, D., MacDonald, R.I., Mondragon, A.

(1999) Cell 98: 523-535

Released	1999-10-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Gallus gallus
Macromolecule	PROTEIN (ALPHA SPECTRIN) (protein)

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1F2V \| pdb_00001f2v	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE OF AEROBIC VITAMIN B12 SYNTHESIS

Shipman, L.W., Li, D., Roessner, C.A., Scott, A.I., Sacchettini, J.C.

(2001) Structure 9: 587-596

Released	2001-07-18
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pseudomonas denitrificans (nom. rej.)
Macromolecule	PRECORRIN-8X METHYLMUTASE (protein)

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1GHQ \| pdb_00001ghq	Download File View File

CR2-C3D COMPLEX STRUCTURE

Szakonyi, G., Guthridge, J.M., Li, D., Holers, V.M., Chen, X.S.

(2001) Science 292: 1725-1728

Released	2001-06-13
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Homo sapiens
Macromolecule	COMPLEMENT C3 (protein) CR2/CD121/C3D/EPSTEIN-BARR VIRUS RECEPTOR (protein)
Unique Ligands	NDG, ZN

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1I1H \| pdb_00001i1h	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE COMPLEX WITH HYDROGENOBYRINIC ACID

Shipman, L.W., Li, D., Roessner, C.A., Scott, A.I., Sacchettini, J.C.

(2001) Structure 9: 587-596

Released	2001-07-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pseudomonas denitrificans (nom. rej.)
Macromolecule	PRECORRIN-8X METHYLMUTASE (protein)
Unique Ligands	COJ

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1N25 \| pdb_00001n25	Download File View File

Crystal structure of the SV40 Large T antigen helicase domain

Li, D., Zhao, R., Lilyestrom, W., Gai, D., Zhang, R., DeCaprio, J.A., Fanning, E., Jochimiak, A., Szakonyi, G., Chen, X.S.

(2003) Nature 423: 512-518

Released	2003-06-03
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Betapolyomavirus macacae
Macromolecule	Large T Antigen (protein)
Unique Ligands	ZN

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1NIX \| pdb_00001nix	Download File View File

THREE DIMENSIONAL SOLUTION STRUCTURE OF HAINANTOXIN-I BY 2D 1H-NMR

Li, D., Liang, S.

(2003) FEBS Lett 555: 616-622

Released	2003-01-14
Method	SOLUTION NMR
Organisms	Haplopelma hainanum
Macromolecule	HAINANTOXIN-I (protein)

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1NIY \| pdb_00001niy	Download File View File

THREE DIMENSIONAL SOLUTION STRUCTURE OF HAINANTOXIN-IV BY 2D 1H-NMR

Li, D., Lu, S., Gu, X., Liang, S.

(2004) J Biological Chem 279: 37734-37740

Released	2003-01-14
Method	SOLUTION NMR
Organisms	Haplopelma hainanum
Macromolecule	HAINANTOXIN-IV (protein)

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1RYG \| pdb_00001ryg	Download File View File

Three dimensional solution structure of the R29A MUTANT of sodium channels inhibitor HAINANTOXIN-IV by 2D 1H-NMR

Li, D., Lu, S., Gu, X., Liang, S.

(2004) J Biological Chem 279: 37734-37740

Released	2004-01-13
Method	SOLUTION NMR
Organisms	Cyriopagopus hainanus
Macromolecule	Hainantoxin-IV (protein)

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1RYV \| pdb_00001ryv	Download File View File

Three dimensional solution structure of the K27A MUTANT of sodium channels inhibitor HAINANTOXIN-IV BY 2D 1H-NMR

Li, D., Lu, S., Gu, X., Liang, S.

(2004) J Biological Chem 279: 37734-37740

Released	2004-01-13
Method	SOLUTION NMR
Organisms	Cyriopagopus hainanus
Macromolecule	Hainantoxin-IV (protein)

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1W6U \| pdb_00001w6u	Download File View File

Structure of human DECR ternary complex

Alphey, M.S., Byres, E., Li, D., Hunter, W.N.

(2005) J Biological Chem 280: 3068

Released	2004-10-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR (protein)
Unique Ligands	HXC, NAP

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2AE9 \| pdb_00002ae9	Download File View File

Solution Structure of the theta subunit of DNA polymerase III from E. coli

Mueller, G.A., Kirby, T.W., Derose, E.F., Li, D., Schaaper, R.M., London, R.E.

(2005) J Bacteriol 187: 7081-7089

Released	2005-10-18
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	DNA polymerase III, theta subunit (protein)

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2D4G \| pdb_00002d4g	Download File View File

Structure of YjcG protein, a putative 2'-5' RNA ligase from Bacillus subtilis

Li, D., Liang, Y.H., Su, X.D.

(2008) Proteins 72: 1071-1076

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus subtilis
Macromolecule	hypothetical protein BSU11850 (protein)

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2RI0 \| pdb_00002ri0	Download File View File

Crystal Structure of glucosamine 6-phosphate deaminase (NagB) from S. mutans

Li, D., Liu, C., Li, L.F., Su, X.D.

(2008) J Mol Biology 379: 73-81

Released	2008-03-25
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptococcus mutans
Macromolecule	Glucosamine-6-phosphate deaminase (protein)
Unique Ligands	BTB, NA

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2RI1 \| pdb_00002ri1	Download File View File

Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P from S. mutans

Liu, C., Li, D., Su, X.D.

(2008) J Mol Biology 379: 73-81

Released	2008-03-25
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Streptococcus mutans
Macromolecule	Glucosamine-6-phosphate deaminase (protein)
Unique Ligands	BTB, GLP

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3AFK \| pdb_00003afk	Download File View File

Crystal Structure of Agrocybe aegerita lectin AAL complexed with Thomsen-Friedenreich antigen

Feng, L., Li, D., Wang, D.

(2010) FASEB J 24: 3861-3868

Released	2010-12-01
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Cyclocybe aegerita
Macromolecule	Anti-tumor lectin (protein)
Unique Ligands	THR
Unique branched monosaccharides	A2G, GAL

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3BR8 \| pdb_00003br8	Download File View File

Crystal structure of acylphosphatase from Bacillus subtilis

Li, D., Hu, J.C., Xia, B., Su, X.D.

To be published

Released	2008-06-24
Method	X-RAY DIFFRACTION 1.33 Å
Organisms	Bacillus subtilis
Macromolecule	Probable acylphosphatase (protein)
Unique Ligands	GOL, PO4

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3H6F \| pdb_00003h6f	Download File View File

Crystal Structure of Mycobacterium Tuberculosis Proteasome Modified by inhibitor HT1171

Li, D., Li, H., Lin, G.

(2009) Nature 461: 621-626

Released	2009-09-15
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Proteasome (Alpha subunit) PrcA (protein) Proteasome (Beta subunit) PrcB (protein)
Unique Ligands	DMF

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3H6I \| pdb_00003h6i	Download File View File

Crystal Structure of Mycobacterium Tuberculosis Proteasome Modified by inhibitor GL1

Li, D., Li, H., Lin, G.

(2009) Nature 461: 621-626

Released	2009-09-15
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Proteasome (Alpha subunit) PrcA (protein) Proteasome (Beta subunit) PrcB (protein)
Unique Ligands	DMF

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3HF9 \| pdb_00003hf9	Download File View File

Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant modified by inhibitor GL1

Li, D., Li, H.

(2009) Nature 461: 621-626

Released	2009-09-15
Method	X-RAY DIFFRACTION 2.878 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Proteasome (Alpha subunit) PrcA (protein) Proteasome (Beta subunit) PrcB (protein)

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3HFA \| pdb_00003hfa	Download File View File

Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant

Li, D., Li, H.

(2009) Nature 461: 621-626

Released	2009-09-15
Method	X-RAY DIFFRACTION 2.504 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Proteasome (Alpha subunit) PrcA (protein) Proteasome (Beta subunit) PrcB (protein)
Unique Ligands	DMF

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3KRD \| pdb_00003krd	Download File View File

Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with Fellutamide B

Li, D., Li, H.

(2010) Arch Biochem Biophys 501: 214-220

Released	2010-09-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mycobacterium tuberculosis synthetic construct
Macromolecule	Fellutamide B (protein) Proteasome subunit alpha (protein) Proteasome subunit beta (protein)
Unique Ligands	HXD

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3M3C \| pdb_00003m3c	Download File View File

Crystal Structure of Agrocybe aegerita lectin AAL complexed with p-Nitrophenyl TF disaccharide

Feng, L., Li, D., Wang, D.

(2010) FASEB J 24: 3861-3868

Released	2010-12-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cyclocybe aegerita
Macromolecule	Anti-tumor lectin (protein)
Unique Ligands	NPO, SO4
Unique branched monosaccharides	A2G, GAL

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3M3E \| pdb_00003m3e	Download File View File

Crystal Structure of Agrocybe aegerita lectin AAL mutant E66A complexed with p-Nitrophenyl Thomsen-Friedenreich disaccharide

Feng, L., Li, D., Wang, D.

(2010) FASEB J 24: 3861-3868

Released	2010-12-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Cyclocybe aegerita
Macromolecule	Anti-tumor lectin (protein)
Unique Ligands	NPO
Unique branched monosaccharides	A2G, GAL

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3M3O \| pdb_00003m3o	Download File View File

Crystal Structure of Agrocybe aegerita lectin AAL mutant R85A complexed with p-Nitrophenyl TF disaccharide

Feng, L., Li, D., Wang, D.

(2010) FASEB J 24: 3861-3868

Released	2010-12-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Cyclocybe aegerita
Macromolecule	Anti-tumor lectin (protein)
Unique Ligands	BTB, NPO
Unique branched monosaccharides	A2G, GAL

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3M3Q \| pdb_00003m3q	Download File View File

Crystal Structure of Agrocybe aegerita lectin AAL complexed with Ganglosides GM1 pentasaccharide

Feng, L., Li, D., Wang, D.

(2010) FASEB J 24: 3861-3868

Released	2010-12-01
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Cyclocybe aegerita
Macromolecule	Anti-tumor lectin (protein)
Unique branched monosaccharides	BGC, GAL, NGA, SIA

1 to 25 of 284 Structures

Page 1 of 12

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1CUN | pdb_00001cun

1F2V | pdb_00001f2v

1GHQ | pdb_00001ghq

1I1H | pdb_00001i1h

1N25 | pdb_00001n25

1NIX | pdb_00001nix

1NIY | pdb_00001niy

1RYG | pdb_00001ryg

1RYV | pdb_00001ryv

1W6U | pdb_00001w6u

2AE9 | pdb_00002ae9

2D4G | pdb_00002d4g

2RI0 | pdb_00002ri0

2RI1 | pdb_00002ri1

3AFK | pdb_00003afk

3BR8 | pdb_00003br8

3H6F | pdb_00003h6f

3H6I | pdb_00003h6i

3HF9 | pdb_00003hf9

3HFA | pdb_00003hfa

3KRD | pdb_00003krd

3M3C | pdb_00003m3c

3M3E | pdb_00003m3e

3M3O | pdb_00003m3o

3M3Q | pdb_00003m3q