RCSB PDB: Search

2LX4 \| pdb_00002lx4	Download File View File

NMR solution structure of peptide a2N(1-17) from Mus musculus V-ATPase

Dip, P., Gruber, G., Marshansky, V.

(2013) J Biological Chem 288: 5896-5913

Released	2013-01-09
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	V-type proton ATPase 116 kDa subunit a isoform 2 (protein)

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3BI3 \| pdb_00003bi3	Download File View File

X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors

Yi, C., Yang, C.-G.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB (protein) DNA (5'-D(DAPDAPDCPDGPDGPDTPDAPDTPDTPDAPDCPDCPDT)-3') (nucleic acid) DNA (5'-D(TPAPGPGPTPAPAP(MA7)PAP(2YR)PCPGPT)-3') (nucleic acid)
Unique Ligands	AKG, MN

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3BIE \| pdb_00003bie	Download File View File

X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG

Yi, C., Yang, C.-G.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 1.68 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB (protein) DNA (5'-D(DAPDAPDCPDGPDGPDTPDTPDTPDTPDAPDCPDCPDT)-3') (nucleic acid) DNA (5'-D(PDAPDGPDGPDTPDAPDAP(MA7)PDAPDCPDCPDGP*DT)-3') (nucleic acid)
Unique Ligands	AKG, MN

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3BKZ \| pdb_00003bkz	Download File View File

X-ray structure of E coli AlkB crosslinked to dsDNA in the active site

Yi, C., Yang, C.-G., He, C.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB (protein) DNA (5'-D(DAPDAPDCPDGPDAPDTPDAPDTPDTPDAPDCPDCPDT)-3') (nucleic acid) DNA (5'-D(DTPDAPDGPDGPDTPDAPDAPDCPDAPDTPDCPDGPDT)-3') (nucleic acid)
Unique Ligands	AKG, MN

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3BTX \| pdb_00003btx	Download File View File

X-ray structure of human ABH2 bound to dsDNA through active site cross-linking

Yang, C.-G., Yi, C., He, C.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) DNA (5'-D(CPTPGPTPAPTP(2YR)PAPTPTPGPCPG)-3') (nucleic acid) DNA (5'-D(DTPDCPDGPDCPDAPDAPDTPDAPDAPDTPDAPDCPDA)-3') (nucleic acid)
Unique Ligands	MG

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3BTY \| pdb_00003bty	Download File View File

Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site

Yang, C.-G., Yi, C., He, C.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) DNA (5'-D(DCPDTPDGPDTPDAPDTP(MA7)PDAPDCPDTPDGPDCPDG)-3') (nucleic acid) DNA (5'-D(DTPDCPDGPDCPDAPDGPDTPDTPDAPDTPDAPDCPDA)-3') (nucleic acid)
Unique Ligands	XL3

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3BTZ \| pdb_00003btz	Download File View File

Crystal structure of human ABH2 cross-linked to dsDNA

Yang, C.-G., Yi, C., He, C.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) DNA (5'-D(APGPGPTPGPAP(2YR)PAPAPTPGPCPG)-3') (nucleic acid) DNA (5'-D(DTPDCPDGPDCPDAPDTPDTPDAPDTPDCPDAPDCPDC)-3') (nucleic acid)

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3BU0 \| pdb_00003bu0	Download File View File

crystal structure of human ABH2 cross-linked to dsDNA with cofactors

Yang, C.-G., Yi, C., He, C.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) DNA (5'-D(CPTPGPTPAPTP(2YR)PAPTPTPGPCPG)-3') (nucleic acid) DNA (5'-D(DTPDCPDGPDCPDAPDAPDTPDAPDAPDTPDAPDCPDA)-3') (nucleic acid)
Unique Ligands	AKG, MN

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3BUC \| pdb_00003buc	Download File View File

X-ray structure of human ABH2 bound to dsDNA with Mn(II) and 2KG

Yang, C.-G., Yi, C., He, C.

(2008) Nature 452: 961-965

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Homo sapiens
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) DNA (5'-D(DCPDTPDGPDTPDAPDTP(MA7)PDAPDCPDTPDGPDCPDG)-3') (nucleic acid) DNA (5'-D(DTPDCPDGPDCPDAPDGPDTPDTPDAPDTPDAPDCPDA)-3') (nucleic acid)
Unique Ligands	AKG, MN, XL3

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3H8O \| pdb_00003h8o	Download File View File

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system

Lu, L., Yi, C., Jian, X., Zheng, Q.

(2010) Nucleic Acids Res 38: 4415-4425

Released	2010-03-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) 5'-D(CPTPGPTPAPTP(2YR)PAPTP(MA7)PGPCPG)-3' (nucleic acid) 5'-D(TPCPGPCPTPAPTPAPAPTPAPCPA)-3' (nucleic acid)
Unique Ligands	GOL

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3H8R \| pdb_00003h8r	Download File View File

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system

Lu, L., Yi, C., Jian, X., Zheng, G., He, C.

(2010) Nucleic Acids Res 38: 4415-4425

Released	2010-03-31
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) 5'-D(CPTPGPTPAPTP(2YR)PAPTP(6MA)PGPCPG)-3' (nucleic acid) 5'-D(TPCPGPCPTPAPTPAPAPTPAPCPA)-3' (nucleic acid)
Unique Ligands	GOL, TRS

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3H8X \| pdb_00003h8x	Download File View File

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system

Lu, L., Yi, C., Jian, X., Zheng, G., He, C.

(2010) Nucleic Acids Res 38: 4415-4425

Released	2010-03-31
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 (protein) 5'-D(CPTPGPTP(ME6)PTP(2YR)PAPTPTPGPCPG)-3' (nucleic acid) 5'-D(TPCPGPCPAPAPTPAPAPGPAPCPA)-3' (nucleic acid)

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3O1M \| pdb_00003o1m	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(TAPGPGPTPAPAP(ME6)PAPCPCPGPT)-3') (nucleic acid)
Unique Ligands	AKG, MN

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3O1O \| pdb_00003o1o	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(TAPGPGPTPAPAP(MFT)PAPCPCPGPT)-3') (nucleic acid)
Unique Ligands	AKG, MN

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3O1P \| pdb_00003o1p	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.51 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(TAPGPGPTPAPAP(EDA)PAPCPCPGPT)-3') (nucleic acid)
Unique Ligands	AKG, GOL, MN

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3O1R \| pdb_00003o1r	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDK)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	AKG, GOL, MN

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3O1S \| pdb_00003o1s	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDQ)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

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3O1T \| pdb_00003o1t	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDU)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

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3O1U \| pdb_00003o1u	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDV)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

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3O1V \| pdb_00003o1v	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDJ)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

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5C6R \| pdb_00005c6r	Download File View File

Crystal structure of PH domain of ASAP1

Xia, D., Tang, W.K.

(2015) Structure 23: 1977-1988

Released	2015-10-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mus musculus
Macromolecule	Arf-GAP (protein)
Unique Ligands	PGE, PO4

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5C79 \| pdb_00005c79	Download File View File

PH domain of ASAP1 in complex with diC4-PtdIns(4,5)P2

Xia, D., Tang, W.K.

(2015) Structure 23: 1977-1988

Released	2015-10-07
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mus musculus
Macromolecule	Arf-GAP (protein)
Unique Ligands	CL, PBU

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8AVZ \| pdb_00008avz	Download File View File

Crystal structure of PksD, the trans-acting acyl hydrolase domain from the bacillaene trans-AT PKS (SeMet derivative)

Fage, C.D., Challis, G.L., Lewandowski, J., Jenner, M.

(2025) JACS Au

Released	2023-08-09
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	Polyketide biosynthesis acyltransferase homolog PksD (protein)
Unique Ligands	ZN

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8AW0 \| pdb_00008aw0	Download File View File

Crystal structure of PksD, the trans-acting acyl hydrolase domain from the bacillaene trans-AT PKS (native)

Fage, C.D., Challis, G.L., Lewandowski, J., Jenner, M.

(2025) JACS Au

Released	2023-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	Polyketide biosynthesis acyltransferase homolog PksD (protein)
Unique Ligands	ZN

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8HTV \| pdb_00008htv	Download File View File

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3a

Su, H.X., Nie, T.Q., Li, M.J., Xu, Y.C.

(2023) J Med Chem 66: 12266-12283

Released	2023-08-30
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase (protein)
Unique Ligands	UZF

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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

2LX4 | pdb_00002lx4

3BI3 | pdb_00003bi3

3BIE | pdb_00003bie

3BKZ | pdb_00003bkz

3BTX | pdb_00003btx

3BTY | pdb_00003bty

3BTZ | pdb_00003btz

3BU0 | pdb_00003bu0

3BUC | pdb_00003buc

3H8O | pdb_00003h8o

3H8R | pdb_00003h8r

3H8X | pdb_00003h8x

3O1M | pdb_00003o1m

3O1O | pdb_00003o1o

3O1P | pdb_00003o1p

3O1R | pdb_00003o1r

3O1S | pdb_00003o1s

3O1T | pdb_00003o1t

3O1U | pdb_00003o1u

3O1V | pdb_00003o1v

5C6R | pdb_00005c6r

5C79 | pdb_00005c79

8AVZ | pdb_00008avz

8AW0 | pdb_00008aw0

8HTV | pdb_00008htv