SMTL ID : 8zb4.1

Crystal structure of NudC from Mycobacterium abscessus in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

13 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: A.191, E.207, E.211, E.253 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.207, A:E.211 CA.2: 5 residues within 4Å: Chain A: E.207, E.210, D.251 Ligands: CA.1, CA.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.207, A:E.210 CA.3: 3 residues within 4Å: Chain A: D.20, E.21 Chain B: E.210 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.21 CA.4: 1 residues within 4Å: Chain A: D.258 No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Chain A: D.92 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.92 CA.6: 4 residues within 4Å: Chain A: E.195, R.206, E.207 Ligands: CA.2 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain B: A.191, E.211 Ligands: NAD.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.191, B:E.211, H2O.2 CA.9: 5 residues within 4Å: Chain B: E.207, E.211, D.251 Ligands: CA.10, NAD.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.207, B:E.211, H2O.2, H2O.2 CA.10: 4 residues within 4Å: Chain B: E.207, E.210 Ligands: CA.9, NAD.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.207 CA.11: 2 residues within 4Å: Chain B: D.20, E.21 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.21 CA.12: 4 residues within 4Å: Chain B: D.88, L.89, D.90 Ligands: CA.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.88, B:L.89 CA.13: 2 residues within 4Å: Chain B: D.90 Ligands: CA.12 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: D.258 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.258

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

NAD.7: 15 residues within 4Å: Chain A: D.160, A.162, W.182, S.188, A.191, G.192, F.193, W.227, S.232, M.234, E.253, W.274, S.289 Chain B: F.156, P.157 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.227 Hydrogen bonds: A:D.160, A:S.188, A:S.188, A:A.191, A:S.232, A:S.232 pi-Stacking: A:F.193, B:F.156, B:F.156 NAD.15: 18 residues within 4Å: Chain A: F.156 Chain B: D.160, A.162, I.164, S.188, L.189, A.191, G.192, F.193, E.207, E.211, W.227, S.232, M.234, S.289 Ligands: CA.8, CA.9, CA.10 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.164 Hydrogen bonds: B:D.160, B:S.188, B:L.189, B:F.193, B:S.232, B:S.232 pi-Stacking: B:F.193, A:F.156, A:F.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meng, L. et al., Structural Studies on Mycobacterial NudC Reveal a Class of Zinc Independent NADH Pyrophosphatase. J.Mol.Biol. (2024)

Release Date

2024-12-11

Peptides

NAD(+) diphosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD(+) diphosphatase

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