SMTL ID : 4kxl.2 (1 other biounit)

Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x 6C6: N-cyclopentyladenosine 5'-(dihydrogen phosphate)(Non-covalent)

6C6.1: 19 residues within 4Å: Chain A: Y.6, C.8, G.9, S.10, I.11, R.12, G.13, H.38, V.39, I.58, N.62, S.80, L.81, G.82, V.83, E.86 Chain B: S.110, A.111, M.112 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.11, A:I.58 Hydrogen bonds: A:G.9, A:I.11, A:R.12, A:G.13, A:N.62, A:S.80, A:S.80, A:L.81, A:G.82, A:V.83 Water bridges: A:Y.6, A:N.62 6C6.3: 20 residues within 4Å: Chain A: S.110, A.111, M.112 Chain B: Y.6, C.8, G.9, S.10, I.11, R.12, G.13, H.38, V.39, E.50, I.58, N.62, S.80, L.81, G.82, V.83, E.86 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.11, B:E.50, B:I.58 Hydrogen bonds: B:Y.6, B:G.9, B:I.11, B:R.12, B:G.13, B:H.38, B:N.62, B:S.80, B:S.80, B:L.81, B:G.82, B:V.83, A:S.110

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.27, R.30 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.27, A:R.30 SO4.4: 2 residues within 4Å: Chain B: R.27, R.30 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.27, B:R.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amiable, C. et al., N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1. Plos One (2013)

Release Date

2014-02-05

Peptides

2'-deoxynucleoside 5'-phosphate N-hydrolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

2'-deoxynucleoside 5'-phosphate N-hydrolase 1

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