SMTL ID : 7ect.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

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

NDP.1: 29 residues within 4Å: Chain A: R.82, H.84, K.102, 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.4, GOL.5, TLA.7 27 PLIP interactions: 27 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:G.230, A:A.233 Salt bridges: A:K.122, A:K.279 pi-Cation interactions: A:K.114 NDP.8: 25 residues within 4Å: Chain B: R.82, H.84, K.102, K.122, D.154, I.155, G.156, R.193, T.197, S.229, G.230, N.231, V.232, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: TLA.10 26 PLIP interactions: 26 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:N.231, B:N.231, B:V.232, B:D.252, B:S.253, B:S.253, B:Q.284, B:A.320, B:T.321, B:N.346, B:N.346 Water bridges: B:G.230, B:A.233 Salt bridges: B:K.122, B:K.279 pi-Cation interactions: B:K.114 NDP.11: 28 residues within 4Å: Chain C: R.82, H.84, K.102, K.122, G.153, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: GOL.13, TLA.18 24 PLIP interactions: 24 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:S.253, C:Q.284, C:A.320, C:N.346, C:N.346 Salt bridges: C:K.122, C:K.279 pi-Cation interactions: C:K.114 NDP.19: 29 residues within 4Å: Chain D: R.82, H.84, K.102, 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.22, GOL.23, TLA.25 27 PLIP interactions: 27 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:G.230, D:A.233 Salt bridges: D:K.122, D:K.279 pi-Cation interactions: D:K.114 NDP.26: 25 residues within 4Å: Chain E: R.82, H.84, K.102, K.122, D.154, I.155, G.156, R.193, T.197, S.229, G.230, N.231, V.232, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: TLA.28 26 PLIP interactions: 26 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:N.231, E:N.231, E:V.232, E:D.252, E:S.253, E:S.253, E:Q.284, E:A.320, E:T.321, E:N.346, E:N.346 Water bridges: E:G.230, E:A.233 Salt bridges: E:K.122, E:K.279 pi-Cation interactions: E:K.114 NDP.29: 28 residues within 4Å: Chain F: R.82, H.84, K.102, K.122, G.153, D.154, I.155, G.156, R.193, T.197, G.228, S.229, G.230, N.231, V.232, D.252, S.253, K.279, Q.284, S.319, A.320, T.321, G.344, S.345, N.346, N.379 Ligands: GOL.31, TLA.36 24 PLIP interactions: 24 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:S.253, F:Q.284, F:A.320, F:N.346, F:N.346 Salt bridges: F:K.122, F:K.279 pi-Cation interactions: F:K.114

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.142, I.144, T.148, R.173 Chain B: N.174 Chain D: R.142 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: W.399, E.403, R.407 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: D.252, S.253, Q.254, G.255, G.303, Q.304, R.305 Ligands: NDP.1 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: G.153, D.154, V.157, G.159, G.182, R.193, N.231 Ligands: NDP.1 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: Q.12, N.323, T.350, Q.351, A.352 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain B: W.399, E.403, R.407 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain C: W.399, E.403, R.407 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain C: D.252, S.253, Q.254, G.255, G.303, Q.304, R.305 Ligands: NDP.11 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain C: R.142 Chain E: R.142, I.144, T.148, R.173 Chain F: N.174 Ligands: GOL.15 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain C: R.142, H.143 Chain E: R.142, H.143 Ligands: GOL.14 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: R.396 Chain B: D.147 Chain C: A.146, E.177, G.178, N.393, S.394, R.396 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain C: E.242, L.243, G.244 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: R.142 Chain D: R.142, I.144, T.148, R.173 Chain E: N.174 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain D: W.399, E.403, R.407 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain D: D.252, S.253, Q.254, G.255, G.303, Q.304, R.305 Ligands: NDP.19 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain D: G.153, D.154, V.157, G.159, G.182, R.193, N.231 Ligands: NDP.19 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain D: Q.12, N.323, T.350, Q.351, A.352 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain E: W.399, E.403, R.407 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain F: W.399, E.403, R.407 Ligand excluded by PLIP GOL.31: 8 residues within 4Å: Chain F: D.252, S.253, Q.254, G.255, G.303, Q.304, R.305 Ligands: NDP.29 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain B: R.142, I.144, T.148, R.173 Chain C: N.174 Chain F: R.142 Ligands: GOL.33 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain B: R.142, H.143 Chain F: R.142, H.143 Ligands: GOL.32 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain D: R.396 Chain E: D.147 Chain F: A.146, E.177, G.178, N.393, S.394, R.396 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain F: E.242, L.243, G.244 Ligand excluded by PLIP

6 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.7: 15 residues within 4Å: Chain A: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, D.154, T.181, R.193, N.346, V.383, S.386 Ligands: NDP.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.80, A:Q.99, A:G.153, A:D.154, A:T.181, A:R.193, A:N.346, A:S.386 Salt bridges: A:K.78, A:K.102, A:K.114, A:R.193 TLA.10: 15 residues within 4Å: Chain B: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, D.154, T.181, R.193, N.346, V.383, S.386 Ligands: NDP.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.80, B:Q.99, B:K.114, B:D.154, B:R.193, B:N.346, B:V.383, B:S.386 Salt bridges: B:K.78, B:K.102, B:K.114, B:R.193 TLA.18: 15 residues within 4Å: Chain C: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, D.154, R.193, N.346, G.382, V.383, S.386 Ligands: NDP.11 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.80, C:Q.99, C:Q.99, C:N.346, C:G.382, C:S.386 Salt bridges: C:K.78, C:K.102, C:K.114, C:R.193 TLA.25: 15 residues within 4Å: Chain D: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, D.154, T.181, R.193, N.346, V.383, S.386 Ligands: NDP.19 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.80, D:Q.99, D:G.153, D:D.154, D:T.181, D:R.193, D:N.346, D:S.386 Salt bridges: D:K.78, D:K.102, D:K.114, D:R.193 TLA.28: 15 residues within 4Å: Chain E: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, D.154, T.181, R.193, N.346, V.383, S.386 Ligands: NDP.26 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.80, E:Q.99, E:K.114, E:D.154, E:R.193, E:N.346, E:V.383, E:S.386 Salt bridges: E:K.78, E:K.102, E:K.114, E:R.193 TLA.36: 15 residues within 4Å: Chain F: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, D.154, R.193, N.346, G.382, V.383, S.386 Ligands: NDP.29 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.80, F:Q.99, F:Q.99, F:N.346, F:G.382, F:S.386 Salt bridges: F:K.78, F:K.102, F:K.114, F:R.193

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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