SMTL ID : 8oov.1

human NME-1 in complex with CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x PAP: 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

PAP.1: 13 residues within 4Å: Chain A: K.32, Y.72, L.75, R.78, F.80, R.108, T.114, R.125, V.132, G.133, N.135, I.137, H.138 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.78, A:T.114, A:T.114, A:R.125, A:N.135, A:N.135 Water bridges: A:K.32, A:R.108, A:R.108, A:T.114, A:G.133, A:H.138, A:G.139 Salt bridges: A:K.32, A:R.108, A:H.138 pi-Stacking: A:F.80, A:F.80 PAP.2: 11 residues within 4Å: Chain B: K.32, Y.72, L.75, R.78, F.80, T.114, R.125, V.132, N.135, I.137, H.138 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.32, B:Y.72, B:R.125, B:N.135 Water bridges: B:R.108, B:R.108, B:R.108, B:R.125, B:G.139 Salt bridges: B:K.32, B:R.78, B:R.78, B:H.138 pi-Stacking: B:F.80, B:F.80 PAP.3: 12 residues within 4Å: Chain C: K.32, Y.72, L.75, R.78, F.80, R.108, T.114, R.125, V.132, N.135, I.137, H.138 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.32, C:T.114, C:T.114, C:R.125, C:N.135 Water bridges: C:R.108, C:R.108, C:T.114, C:R.125, C:G.139, A:E.172 Salt bridges: C:K.32, C:R.78, C:R.108, C:H.138 pi-Stacking: C:F.80, C:F.80

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 3 residues within 4Å: Chain C: V.160, D.161, Y.162 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tossounian, M.A. et al., A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1. Int J Mol Sci (2023)

Release Date

2023-06-07

Peptides

Nucleoside diphosphate kinase A: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Nucleoside diphosphate kinase A

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