SMTL ID : 7ecs.1

Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Malonate and NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-hexamer

Ligands

48 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: W.399, E.403, R.407 Ligand excluded by PLIP GOL.2: 6 residues within 4Å: Chain A: L.397, S.398, W.399, T.400, E.403 Chain C: R.407 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: R.142, I.144, T.148 Chain B: N.174 Chain D: R.142 Ligands: GOL.4, GOL.37 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: R.142 Chain D: R.142, H.143 Ligands: GOL.3, GOL.36, GOL.37 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: A.104, L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: T.447, K.448, A.451 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain B: R.142, H.143 Chain F: R.142, H.143 Ligands: GOL.14, GOL.19 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: W.399, E.403, R.407 Ligands: GOL.13 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: R.407 Chain B: L.397, S.398, W.399, T.400, E.403 Ligands: GOL.12 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: R.142 Chain D: N.174 Chain F: R.142, I.144, T.148 Ligands: GOL.11 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: E.217, S.218, A.220, G.221, K.222, D.314 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain B: T.447, K.448, A.451 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: Q.12, N.323, T.350, Q.351 Ligands: MLI.20 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: A.104, L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: R.142, I.144, T.148, R.173 Chain C: N.174 Chain F: R.142 Ligands: GOL.11 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain C: W.399, E.403, R.407 Ligands: GOL.24 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: R.407 Chain C: L.397, S.398, W.399, T.400, E.403 Ligands: GOL.23 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain C: A.104, L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain C: Q.12, N.323, T.350, Q.351 Ligands: MLI.31 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: H.211, G.366, G.432, L.434, P.435 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: D.252, S.253, G.255, G.303, Q.304, R.305 Ligands: NDP.33 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: V.52, W.53 Chain E: W.460 Chain F: R.130, V.134, K.171 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain C: C.141, R.142, R.173 Chain F: C.141, L.172, R.173 Ligands: GOL.63 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain D: W.399, E.403, R.407 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain D: L.397, S.398, W.399, T.400, E.403 Chain F: R.407 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain A: R.142 Chain D: R.142, I.144, T.148 Chain E: N.174 Ligands: GOL.4, GOL.37 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain A: R.142, H.143 Chain D: R.142 Ligands: GOL.3, GOL.4, GOL.36 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain D: A.104, L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain D: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain D: T.447, K.448, A.451 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain C: R.142, H.143 Chain E: R.142, H.143 Ligands: GOL.47, GOL.52 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain E: W.399, E.403, R.407 Ligands: GOL.46 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain D: R.407 Chain E: L.397, S.398, W.399, T.400, E.403 Ligands: GOL.45 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain A: N.174 Chain C: R.142, I.144, T.148 Chain E: R.142 Ligands: GOL.44 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain E: E.217, S.218, A.220, G.221, K.222, D.314 Ligand excluded by PLIP GOL.49: 3 residues within 4Å: Chain E: T.447, K.448, A.451 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain E: Q.12, N.323, T.350, Q.351 Ligands: MLI.53 Ligand excluded by PLIP GOL.51: 7 residues within 4Å: Chain E: A.104, L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.52: 7 residues within 4Å: Chain C: R.142 Chain E: R.142, I.144, T.148, R.173 Chain F: N.174 Ligands: GOL.44 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain F: W.399, E.403, R.407 Ligands: GOL.57 Ligand excluded by PLIP GOL.57: 7 residues within 4Å: Chain E: R.407 Chain F: L.397, S.398, W.399, T.400, E.403 Ligands: GOL.56 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain F: A.104, L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.59: 5 residues within 4Å: Chain F: Q.12, N.323, T.350, Q.351 Ligands: MLI.64 Ligand excluded by PLIP GOL.60: 5 residues within 4Å: Chain F: H.211, G.366, G.432, L.434, P.435 Ligand excluded by PLIP GOL.61: 7 residues within 4Å: Chain F: D.252, S.253, G.255, G.303, Q.304, R.305 Ligands: NDP.66 Ligand excluded by PLIP GOL.62: 6 residues within 4Å: Chain B: W.460 Chain C: R.130, V.134, K.171 Chain F: V.52, W.53 Ligand excluded by PLIP GOL.63: 7 residues within 4Å: Chain C: C.141, L.172, R.173 Chain F: C.141, R.142, R.173 Ligands: GOL.30 Ligand excluded by PLIP

12 x MLI: MALONATE ION(Non-functional Binders)

MLI.8: 10 residues within 4Å: Chain A: G.79, G.80, Q.99, K.102, K.114, A.152, D.154, N.346, V.383 Ligands: NDP.10 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.80, A:Q.99, A:D.154, A:N.346 Water bridges: A:K.114, A:N.379 Salt bridges: A:K.102, A:K.114, A:K.114 MLI.9: 5 residues within 4Å: Chain A: S.326, G.327, E.328, T.350, A.352 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.326, A:G.327, A:E.328, A:T.350 Water bridges: A:E.328, A:E.328, A:A.352 MLI.20: 6 residues within 4Å: Chain B: S.326, G.327, E.328, T.350, A.352 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.327, B:E.328, B:T.350 Water bridges: B:Q.351 MLI.21: 8 residues within 4Å: Chain B: G.79, G.80, Q.99, K.102, K.114, D.154, N.346 Ligands: NDP.22 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.80, B:Q.99, B:Q.99, B:D.154, B:N.346 Water bridges: B:K.114, B:G.153, B:N.379 Salt bridges: B:K.102, B:K.114, B:K.114 MLI.31: 6 residues within 4Å: Chain C: S.326, G.327, E.328, T.350, A.352 Ligands: GOL.26 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.326, C:G.327, C:E.328 Water bridges: C:E.328, C:Q.351 MLI.32: 10 residues within 4Å: Chain C: G.79, G.80, Q.99, K.102, K.114, A.152, D.154, N.346, V.383 Ligands: NDP.33 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.80, C:Q.99, C:D.154, C:R.193, C:N.346 Water bridges: C:K.114, C:G.153 Salt bridges: C:K.102, C:K.114, C:K.114 MLI.41: 10 residues within 4Å: Chain D: G.79, G.80, Q.99, K.102, K.114, A.152, D.154, N.346, V.383 Ligands: NDP.43 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.80, D:Q.99, D:D.154, D:N.346 Water bridges: D:K.114, D:N.379 Salt bridges: D:K.102, D:K.114, D:K.114 MLI.42: 5 residues within 4Å: Chain D: S.326, G.327, E.328, T.350, A.352 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.326, D:G.327, D:E.328, D:T.350 Water bridges: D:E.328, D:E.328, D:A.352 MLI.53: 6 residues within 4Å: Chain E: S.326, G.327, E.328, T.350, A.352 Ligands: GOL.50 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.327, E:E.328, E:T.350 Water bridges: E:Q.351 MLI.54: 8 residues within 4Å: Chain E: G.79, G.80, Q.99, K.102, K.114, D.154, N.346 Ligands: NDP.55 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.80, E:Q.99, E:Q.99, E:D.154, E:N.346 Water bridges: E:K.114, E:G.153, E:N.379 Salt bridges: E:K.102, E:K.114, E:K.114 MLI.64: 6 residues within 4Å: Chain F: S.326, G.327, E.328, T.350, A.352 Ligands: GOL.59 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.326, F:G.327, F:E.328 Water bridges: F:E.328, F:Q.351 MLI.65: 10 residues within 4Å: Chain F: G.79, G.80, Q.99, K.102, K.114, A.152, D.154, N.346, V.383 Ligands: NDP.66 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.80, F:Q.99, F:D.154, F:R.193, F:N.346 Water bridges: F:K.114, F:G.153 Salt bridges: F:K.102, F:K.114, F:K.114

6 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.10: 26 residues within 4Å: Chain A: R.82, H.84, K.122, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, S.251, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: MLI.8 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:T.197, A:V.232, A:N.379 Hydrogen bonds: A:R.82, A:H.84, A:D.154, A:G.156, A:R.193, A:R.193, A:T.197, A:S.229, A:S.229, A:N.231, A:N.231, A:V.232, A:S.253, A:S.253, A:Q.284, A:A.320, A:T.321, A:N.346, A:N.346 Water bridges: A:R.82, A:K.122, A:K.122, A:D.154, A:T.197, A:G.230, A:A.233, A:S.253, A:K.279, A:K.279 Salt bridges: A:K.122, A:K.279 NDP.22: 26 residues within 4Å: Chain B: R.82, H.84, K.122, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, S.251, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: MLI.21 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:T.197, B:V.232, B:N.379 Hydrogen bonds: B:R.82, B:H.84, B:D.154, B:G.156, B:R.193, B:R.193, B:S.229, B:S.229, B:N.231, B:N.231, B:V.232, B:D.252, B:S.253, B:Q.284, B:A.320, B:T.321, B:N.346, B:N.346 Water bridges: B:R.82, B:D.154, B:T.197, B:G.230, B:A.233, B:K.279, B:K.279 Salt bridges: B:K.122, B:K.279 NDP.33: 27 residues within 4Å: Chain C: R.82, H.84, K.122, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, S.251, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: GOL.28, MLI.32 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:T.197, C:V.232, C:N.379 Hydrogen bonds: C:R.82, C:H.84, C:D.154, C:G.156, C:R.193, C:R.193, C:S.229, C:S.229, C:N.231, C:N.231, C:V.232, C:D.252, C:S.253, C:Q.284, C:A.320, C:N.346, C:N.346 Water bridges: C:R.82, C:D.154, C:D.154, C:V.157, C:T.197, C:G.230, C:A.233, C:K.279 Salt bridges: C:K.122, C:K.279 NDP.43: 26 residues within 4Å: Chain D: R.82, H.84, K.122, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, S.251, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: MLI.41 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:T.197, D:V.232, D:N.379 Hydrogen bonds: D:R.82, D:H.84, D:D.154, D:G.156, D:R.193, D:R.193, D:T.197, D:S.229, D:S.229, D:N.231, D:N.231, D:V.232, D:S.253, D:S.253, D:Q.284, D:A.320, D:T.321, D:N.346, D:N.346 Water bridges: D:R.82, D:K.122, D:K.122, D:D.154, D:T.197, D:G.230, D:A.233, D:S.253, D:K.279, D:K.279 Salt bridges: D:K.122, D:K.279 NDP.55: 26 residues within 4Å: Chain E: R.82, H.84, K.122, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, S.251, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: MLI.54 30 PLIP interactions: 30 interactions with chain E Hydrophobic interactions: E:T.197, E:V.232, E:N.379 Hydrogen bonds: E:R.82, E:H.84, E:D.154, E:G.156, E:R.193, E:R.193, E:S.229, E:S.229, E:N.231, E:N.231, E:V.232, E:D.252, E:S.253, E:Q.284, E:A.320, E:T.321, E:N.346, E:N.346 Water bridges: E:R.82, E:D.154, E:T.197, E:G.230, E:A.233, E:K.279, E:K.279 Salt bridges: E:K.122, E:K.279 NDP.66: 27 residues within 4Å: Chain F: R.82, H.84, K.122, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, S.251, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: GOL.61, MLI.65 30 PLIP interactions: 30 interactions with chain F Hydrophobic interactions: F:T.197, F:V.232, F:N.379 Hydrogen bonds: F:R.82, F:H.84, F:D.154, F:G.156, F:R.193, F:R.193, F:S.229, F:S.229, F:N.231, F:N.231, F:V.232, F:D.252, F:S.253, F:Q.284, F:A.320, F:N.346, F:N.346 Water bridges: F:R.82, F:D.154, F:D.154, F:V.157, F:T.197, F:G.230, F:A.233, F:K.279 Salt bridges: F:K.122, F:K.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godsora, B.K.J. et al., Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites. Proteins (2022)

Release Date

2021-12-08

Peptides

Glutamate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Glutamate dehydrogenase

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