SMTL ID : 6nfl.1

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G complexed with 2-HP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x L60: 1,3-diazinan-2-one(Non-covalent)

L60.1: 9 residues within 4Å: Chain A: R.25, R.26, R.27, Q.28, T.29, N.55, H.60, W.88, F.92 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.88 Hydrogen bonds: A:T.29, A:N.55, A:H.60 Water bridges: A:T.29, A:T.29, A:T.29 pi-Stacking: A:W.88

1 x 71O: pyrimidin-2-ol(Non-covalent)

71O.2: 7 residues within 4Å: Chain A: E.34, F.85, R.113, K.115, D.146, E.147, Y.150 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.147 Hydrogen bonds: A:R.113

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

CL.3: 5 residues within 4Å: Chain A: S.141, I.142, S.177, L.180, R.181 Ligand excluded by PLIP

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

EDO.4: 2 residues within 4Å: Chain A: E.149, D.153 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.153 EDO.5: 4 residues within 4Å: Chain A: T.144, Y.145, D.146, E.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.144 EDO.6: 1 residues within 4Å: Chain A: L.186 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B. Faseb Bioadv (2020)

Release Date

2019-12-25

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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