SMTL ID : 6m61.1

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: K.163, V.164, D.167, N.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.167, A:N.168, A:N.168 EDO.2: 3 residues within 4Å: Chain A: D.40, L.41, N.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.40, A:L.41, A:N.42, A:N.42 Water bridges: A:Y.43 EDO.8: 5 residues within 4Å: Chain B: P.130, M.131, F.132, N.137, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.131, B:N.137 EDO.9: 4 residues within 4Å: Chain B: G.89, D.90, G.115, G.116 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.90, B:D.90 Water bridges: B:D.90 EDO.10: 4 residues within 4Å: Chain B: D.40, L.41, I.77, Q.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.41 EDO.11: 5 residues within 4Å: Chain A: Y.50 Chain B: T.278, H.280, V.282, F.287 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.50, B:T.278, B:H.280 Water bridges: B:Y.277, B:D.290, B:D.290 EDO.12: 4 residues within 4Å: Chain B: P.253, K.255, D.258, D.306 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.255, B:D.306, B:D.306 EDO.16: 4 residues within 4Å: Chain C: T.278, H.280, F.287 Chain D: Y.50 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.50, C:H.280 Water bridges: D:K.56, C:D.290, C:D.290 EDO.17: 5 residues within 4Å: Chain C: R.21, N.25, F.57, H.58, F.319 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.21, C:N.25, C:H.58 EDO.18: 3 residues within 4Å: Chain C: K.255, N.305, D.306 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.255, C:D.306 EDO.21: 4 residues within 4Å: Chain D: Y.256, G.301, I.302, A.303 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.303, D:A.303

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: A.129, P.130, M.131, F.132, N.137, K.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.131, A:N.137 Water bridges: A:K.140

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 1 residues within 4Å: Chain A: H.58 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.58, H2O.3 ZN.5: 2 residues within 4Å: Chain A: D.290, H.292 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.290, A:D.290, A:H.292, H2O.4, H2O.10 ZN.13: 2 residues within 4Å: Chain B: D.290, H.292 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.290, B:H.292, H2O.18, H2O.20, H2O.23 ZN.19: 1 residues within 4Å: Chain C: E.336 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.336, H2O.32, H2O.34 ZN.20: 2 residues within 4Å: Chain C: D.290, H.292 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.290, C:H.292, H2O.30, H2O.33, H2O.36

2 x F4F: (5aS,6R,9S,9aS)-9-methyl-9-oxidanyl-1-oxidanylidene-6-propan-2-yl-3,5a,6,7,8,9a-hexahydro-2-benzoxepine-4-carboxylic acid(Covalent)

F4F.6: 13 residues within 4Å: Chain A: P.125, S.152, C.153, T.154, T.178, H.180, T.183, T.212, G.213, A.214, A.233, R.235 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.125, A:T.178, A:T.183, A:A.233 Hydrogen bonds: A:C.153, A:G.213, A:A.214 F4F.14: 13 residues within 4Å: Chain B: P.125, S.152, C.153, T.154, T.178, H.180, T.183, T.212, G.213, A.214, A.233, R.235 Ligands: NAD.15 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.125, B:T.178, B:T.183, B:A.233 Hydrogen bonds: B:S.152, B:S.152, B:C.153, B:T.212, B:G.213 Water bridges: B:S.152

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

NAD.7: 26 residues within 4Å: Chain A: N.10, G.11, F.12, G.13, R.14, I.15, N.35, D.36, P.37, F.38, I.39, E.80, R.81, S.99, T.100, G.101, F.103, S.123, A.124, C.153, A.184, N.317, E.318, Y.321 Chain D: P.192 Ligands: F4F.6 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.15, A:I.15, A:Y.321 Hydrogen bonds: A:N.10, A:F.12, A:R.14, A:I.15, A:N.35, A:R.81, A:N.317 Water bridges: A:G.13, A:G.16, A:R.17, A:G.101, A:S.123, A:A.184, A:A.184, A:E.318, A:E.318 pi-Stacking: A:F.38 NAD.15: 26 residues within 4Å: Chain B: N.10, G.11, F.12, G.13, R.14, I.15, N.35, D.36, P.37, F.38, I.39, E.80, R.81, S.99, T.100, G.101, F.103, S.123, A.124, C.153, A.184, N.317, E.318, Y.321 Chain C: P.192 Ligands: F4F.14 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.15, B:I.15, B:Y.321 Hydrogen bonds: B:N.10, B:F.12, B:F.12, B:R.14, B:I.15, B:N.35, B:R.81, B:N.317 Water bridges: B:F.12, B:G.13, B:G.16, B:R.17, B:G.101, B:S.123 pi-Stacking: B:F.38

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 5 residues within 4Å: Chain B: Q.281 Chain D: G.194, K.195, L.196, W.197 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.197 Water bridges: D:G.194, D:W.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y. et al., Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance. Chem Sci (2020)

Release Date

2020-12-30

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
Q

C
P

D
R

Glyceraldehyde-3-phosphate dehydrogenase