SMTL ID : 7e44.2 (1 other biounit)

Crystal structure of NudC complexed with dpCoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x COD: DEPHOSPHO COENZYME A(Non-covalent)

COD.1: 15 residues within 4Å: Chain A: A.130, I.134, H.148, H.151, T.157, V.158, A.160, F.162, Q.194, W.196, P.237, T.241, A.243 Chain B: E.113, Y.126 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.157 Water bridges: A:Q.128, A:A.160, B:P.127, B:P.127 Salt bridges: A:H.151, A:H.151 pi-Stacking: A:F.162, A:F.162, B:Y.126, B:Y.126 Hydrogen bonds: B:E.113, B:Y.126, B:Y.126 COD.3: 11 residues within 4Å: Chain A: E.113, Y.126 Chain B: I.134, H.151, A.160, F.162, W.196, M.203, T.241, V.242, A.243 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.160 Hydrogen bonds: B:H.151, A:E.113, A:Y.126 pi-Stacking: B:F.162, B:F.162, A:Y.126 Water bridges: A:P.127, A:P.127

2 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, W. et al., Structural insights into dpCoA-RNA decapping by NudC. Rna Biol. (2021)

Release Date

2021-07-28

Peptides

NADH pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

NADH pyrophosphatase

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