SMTL ID : 8zb5.1

Crystal structure of NudC from Mycobacterium abscessus in complex with AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

13 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: A.191, E.211, E.253 Ligands: AMP.8 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:A.191, A:E.211, H2O.1, AMP.8 CA.2: 4 residues within 4Å: Chain A: E.195, R.206, E.207 Ligands: AMP.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.207, H2O.1 CA.3: 2 residues within 4Å: Chain A: D.20, E.21 No protein-ligand interaction detected (PLIP) CA.4: 6 residues within 4Å: Chain A: E.207, E.210, E.211, D.251, E.253 Ligands: AMP.8 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.207, A:E.211, A:D.251, H2O.1, AMP.8 CA.5: 1 residues within 4Å: Chain A: D.258 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.258 CA.6: 2 residues within 4Å: Chain A: D.90, D.92 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.92 CA.7: 1 residues within 4Å: Chain A: F.193 No protein-ligand interaction detected (PLIP) CA.10: 4 residues within 4Å: Chain B: F.193, E.195, E.207 Ligands: CA.15 No protein-ligand interaction detected (PLIP) CA.11: 5 residues within 4Å: Chain B: A.191, E.207, E.211, E.253 Ligands: CA.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.211 CA.12: 1 residues within 4Å: Chain B: D.92 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.92 CA.13: 1 residues within 4Å: Chain B: F.193 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: E.21 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.21 CA.15: 6 residues within 4Å: Chain B: E.207, E.210, D.251, E.253 Ligands: CA.10, CA.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.210, B:D.251

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.8: 12 residues within 4Å: Chain A: D.160, A.191, G.192, F.193, E.207, E.211, E.253 Chain B: F.156, P.157 Ligands: CA.1, CA.2, CA.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.160, A:F.193, A:E.207 pi-Stacking: A:F.193, B:F.156, B:F.156 AMP.16: 5 residues within 4Å: Chain A: F.156, P.157 Chain B: R.158, D.160, F.193 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.158, B:D.160 pi-Stacking: B:F.193, A:F.156

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 2 residues within 4Å: Chain A: E.35, D.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.58 TRS.17: 3 residues within 4Å: Chain B: A.34, E.35, D.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.34, B:D.58

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
B

B
A

NAD(+) diphosphatase

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