SMTL ID : 6c4t.1

Staphylopine dehydrogenase (SaODH) - NADP+ bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x NA7: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

NA7.1: 21 residues within 4Å: Chain A: G.26, T.27, G.28, P.29, V.30, A.31, R.51, S.55, K.57, S.58, V.95, A.108, C.109, T.110, A.111, A.113, D.116, T.117, S.136, R.374, E.378 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:G.28, A:V.30, A:S.55, A:S.58, A:S.58, A:S.58, A:S.58, A:A.108, A:D.116, A:S.136, A:R.374 Salt bridges: A:R.51, A:K.57, A:K.57, A:R.374, A:R.374 pi-Cation interactions: A:R.51 NA7.3: 21 residues within 4Å: Chain B: G.26, T.27, G.28, P.29, V.30, A.31, R.51, S.55, K.57, S.58, V.95, A.108, C.109, T.110, A.111, A.113, D.116, T.117, S.136, R.374, E.378 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.27, B:T.27, B:G.28, B:V.30, B:S.55, B:S.58, B:S.58, B:S.58, B:S.58, B:A.108, B:D.116, B:S.136, B:R.374 Salt bridges: B:R.51, B:K.57, B:K.57, B:R.374, B:R.374 pi-Cation interactions: B:R.51

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Q.119, Q.120, L.121, S.122, L.123, L.126, F.148, F.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.119 GOL.4: 8 residues within 4Å: Chain B: Q.119, Q.120, L.121, S.122, L.123, L.126, F.148, F.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McFarlane, J.S. et al., Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. J. Biol. Chem. (2018)

Release Date

2018-04-11

Peptides

Staphylopine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Staphylopine dehydrogenase

Related Entries With Identical Sequence