SMTL ID : 5isy.1

Crystal structure of Nudix family protein with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.100, C.103, C.118, C.121 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.100, A:C.103 ZN.3: 4 residues within 4Å: Chain B: C.100, C.103, C.118, C.121 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.100, B:C.103, B:C.118, B:C.121

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 15 residues within 4Å: Chain A: A.130, C.132, I.134, A.160, F.162, Q.194, W.196, F.198, S.201, M.203, T.241, V.242, A.243 Chain B: E.113, Y.126 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.134 Hydrogen bonds: A:Q.194, A:F.198, A:S.201, A:S.201, A:V.242, A:A.243, B:Y.126 Water bridges: A:Q.128, A:V.163, A:Q.200, B:P.127, B:P.127 pi-Stacking: A:F.162, A:F.162, B:Y.126, B:Y.126 NAD.4: 14 residues within 4Å: Chain A: E.113, Y.126 Chain B: A.130, C.132, I.134, F.162, W.196, F.198, S.201, M.203, E.221, T.241, V.242, A.243 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.134 Hydrogen bonds: B:W.196, B:F.198, B:S.201, B:V.242, B:A.243, A:E.113, A:Y.126 pi-Stacking: B:F.162, B:F.162, A:Y.126, A:Y.126 Water bridges: A:P.127, A:P.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Structural basis of prokaryotic NAD-RNA decapping by NudC. Cell Res. (2016)

Release Date

2016-09-14

Peptides

NADH pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

NADH pyrophosphatase

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