SMTL ID : 8gv3.1

The cryo-EM structure of GSNOR with NYY001

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.97, G.98, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:C.100, A:C.103, A:C.111 ZN.2: 4 residues within 4Å: Chain A: C.45, H.67, C.174 Ligands: WKZ.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.45, A:H.67, A:C.174 ZN.5: 5 residues within 4Å: Chain B: C.97, G.98, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.97, B:C.100, B:C.103, B:C.111 ZN.6: 4 residues within 4Å: Chain B: C.45, H.67, C.174 Ligands: WKZ.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.45, B:H.67, B:C.174

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

NAD.3: 21 residues within 4Å: Chain A: H.46, Y.93, C.174, T.178, G.199, G.201, G.202, V.203, D.223, I.224, C.268, I.269, V.274, V.292, G.293, V.294, T.317, A.318, F.319, R.369 Ligands: WKZ.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.178 Hydrogen bonds: A:H.46, A:L.200, A:G.202, A:V.203, A:D.223, A:I.224, A:I.269, A:V.294, A:T.317, A:F.319 Salt bridges: A:R.369 NAD.7: 21 residues within 4Å: Chain B: H.46, Y.93, C.174, T.178, G.199, G.201, G.202, V.203, D.223, I.224, C.268, I.269, V.274, V.292, G.293, V.294, T.317, A.318, F.319, R.369 Ligands: WKZ.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.178 Hydrogen bonds: B:H.46, B:L.200, B:G.202, B:V.203, B:D.223, B:I.224, B:I.269, B:V.294, B:T.317, B:F.319 Salt bridges: B:R.369

2 x WKZ: (4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thiazolidin-3-yl)propyl]-1H-pyrrol-1-yl}-3-methylbenzamide(Non-covalent)

WKZ.4: 17 residues within 4Å: Chain A: C.45, T.47, H.67, Y.93, I.94, P.95, L.110, C.111, Q.112, Q.118, M.141, C.174, A.318 Chain B: F.306, T.310 Ligands: ZN.2, NAD.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.306, B:T.310, A:Y.93, A:A.318 Hydrogen bonds: A:Q.112 WKZ.8: 17 residues within 4Å: Chain A: F.306, T.310 Chain B: C.45, T.47, H.67, Y.93, I.94, P.95, L.110, C.111, Q.112, Q.118, M.141, C.174, A.318 Ligands: ZN.6, NAD.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.93, B:A.318, A:F.306, A:T.310 Hydrogen bonds: B:Q.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., The cryo-EM structure of GSNOR with NYY001. To Be Published

Release Date

2023-09-20

Peptides

Alcohol dehydrogenase class-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase class-3