SMTL ID : 5iw4.1

Crystal structure of E. coli NudC in complex with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.99, C.102, C.117, C.120 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.117, A:C.120 ZN.3: 4 residues within 4Å: Chain B: C.99, C.102, C.117, C.120 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.99, B:C.102, B:C.117, B:C.120

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

NAD.2: 15 residues within 4Å: Chain A: A.129, C.131, I.133, R.149, F.161, Q.193, W.195, F.197, S.200, M.202, T.240, V.241, A.242 Chain B: E.112, Y.125 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.133 Hydrogen bonds: A:Q.193, A:S.200, A:S.200, A:T.240, A:V.241, A:A.242 Water bridges: A:A.159, A:F.161, A:F.161 pi-Stacking: A:F.161, A:F.161, B:Y.125, B:Y.125 NAD.4: 12 residues within 4Å: Chain A: Y.125 Chain B: A.129, C.131, A.159, F.161, W.195, F.197, S.200, M.202, T.240, V.241, A.242 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.200, B:T.240, B:V.241, B:A.242 pi-Stacking: B:F.161, B:F.161, A:Y.125, A:Y.125 Water bridges: A:P.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofer, K. et al., Structure and function of the bacterial decapping enzyme NudC. Nat.Chem.Biol. (2016)

Release Date

2016-07-13

Peptides

NADH pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH pyrophosphatase

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