SMTL ID : 5cqh.1

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.60, E.62, C.91, C.96 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.60, A:C.91, A:C.96

1 x DC: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DC.2: 4 residues within 4Å: Chain A: D.121, Y.126, K.127, R.179 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.121 Water bridges: A:R.179, A:R.179 Salt bridges: A:K.127 pi-Cation interactions: A:R.179

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: S.141, I.142, S.177, R.181 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: R.59, L.63, W.94, E.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:E.99 Water bridges: A:R.59 EDO.5: 10 residues within 4Å: Chain A: T.29, H.60, E.62, W.88, S.89, P.90, C.91, C.96, Y.120 Ligands: ZN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.29, A:C.91 Water bridges: A:T.29 EDO.6: 4 residues within 4Å: Chain A: Y.30, F.52, C.54, E.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.30 EDO.7: 3 residues within 4Å: Chain A: D.146, E.147, Y.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.115, A:E.147 Water bridges: A:R.113, A:R.113

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

Related Entries With Identical Sequence