SMTL ID : 5cqk.1

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.60, E.62, C.91, W.94, C.96 Ligands: GOL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.60, A:C.91, A:C.96, H2O.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: R.26, R.27, Q.28, T.29, N.55, H.60, E.62, W.88, C.91, Y.120 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.27, A:T.29, A:N.55 Water bridges: A:T.29, A:N.55, A:E.62, A:E.62, A:S.89 GOL.3: 9 residues within 4Å: Chain A: Y.6, M.8, T.12, Y.30, F.52, L.53, C.54, E.56, R.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.30 Water bridges: A:Y.6, A:T.12

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: R.59, L.66, D.67, P.70 Ligands: PGE.5, NA.6 No protein-ligand interaction detected (PLIP) PGE.5: 7 residues within 4Å: Chain A: R.59, L.63, L.66, D.67, E.99 Ligands: PGE.4, NA.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:R.59, A:D.67

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: R.59, D.67 Ligands: PGE.4, PGE.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. J.Biol.Chem. (2015)

Release Date

2015-10-07

Peptides

DNA dC->dU-editing enzyme APOBEC-3B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA dC->dU-editing enzyme APOBEC-3B

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