SMTL ID : 6p2i.1

Acyclic imino acid reductase (Bsp5) in complex with NADPH and D-Arg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 25 residues within 4Å: Chain A: T.74, S.75, P.95, S.98, V.102, G.149, I.150, G.151, Q.152, I.153, L.171, N.172, K.173, S.174, R.176, H.199, I.200, P.201, T.206, T.227, C.228, D.253, A.276, W.277 Ligands: DAR.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:V.102, A:I.153 Hydrogen bonds: A:I.150, A:I.150, A:G.151, A:Q.152, A:I.153, A:K.173, A:S.174, A:D.253, A:D.253, A:W.277 Water bridges: A:S.75, A:Q.152, A:Q.152, A:G.154, A:N.172, A:N.172, A:K.173, A:R.176, A:R.202, A:R.202, A:N.203, A:N.203, A:D.205 Salt bridges: A:K.173, A:R.176 pi-Cation interactions: A:K.173 NAP.5: 25 residues within 4Å: Chain B: T.74, S.75, P.95, S.98, V.102, G.149, I.150, G.151, Q.152, I.153, L.171, N.172, K.173, S.174, R.176, H.199, I.200, P.201, T.206, T.227, C.228, D.253, A.276, W.277 Ligands: DAR.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.102, B:I.153, B:W.277 Hydrogen bonds: B:I.150, B:I.150, B:G.151, B:Q.152, B:I.153, B:K.173, B:K.173, B:S.174, B:D.253, B:W.277 Water bridges: B:S.75, B:D.77, B:G.154, B:N.172, B:N.172, B:K.173, B:R.202, B:R.202, B:N.203, B:N.203, B:D.205 Salt bridges: B:R.176

2 x DAR: D-ARGININE(Non-covalent)

DAR.2: 10 residues within 4Å: Chain A: E.51, I.72, T.73, T.74, S.75, Y.97, R.229, W.277, N.286 Ligands: NAP.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.73 Hydrogen bonds: A:T.74, A:T.74, A:S.75, A:S.75, A:S.75, A:S.75, A:Y.97, A:R.229, A:N.286, A:N.286 Water bridges: A:Y.11, A:R.229, B:Y.132 Salt bridges: A:E.51 pi-Cation interactions: A:W.277 DAR.6: 10 residues within 4Å: Chain B: E.51, I.72, T.73, T.74, S.75, Y.97, R.229, W.277, N.286 Ligands: NAP.5 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.73 Hydrogen bonds: B:T.74, B:T.74, B:S.75, B:S.75, B:S.75, B:Y.97, B:Y.97, B:R.229, B:N.286, B:N.286 Water bridges: B:R.229, A:Y.132 Salt bridges: B:E.51 pi-Cation interactions: B:W.277

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: R.141, F.164, Q.165 Chain B: Q.100, T.156, E.159, I.160 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.141, A:F.164, B:Q.100 Water bridges: B:Q.100 EDO.4: 1 residues within 4Å: Chain A: W.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.15 Water bridges: A:E.284 EDO.7: 6 residues within 4Å: Chain A: Q.100, T.156, I.160 Chain B: R.141, A.163, F.164 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.100, B:R.141, B:F.164 Water bridges: A:Q.100, A:T.156 EDO.8: 6 residues within 4Å: Chain B: I.55, T.56, D.77, Y.78, I.79, D.80 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, J. et al., An Asymmetric Reductase That Intercepts Acyclic Imino Acids Producedin Situby a Partner Oxidase. J.Am.Chem.Soc. (2019)

Release Date

2019-07-24

Peptides

Glycerate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerate dehydrogenase