SMTL ID : 7ecr.1

Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-hexamer

Ligands

40 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: R.142, I.144, T.148 Chain B: N.174 Chain D: R.142 Ligands: GOL.5, GOL.31 Ligand excluded by PLIP GOL.2: 3 residues within 4Å: Chain A: W.399, E.403, R.407 Ligand excluded by PLIP GOL.3: 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.4: 5 residues within 4Å: Chain A: L.397, S.398, W.399, E.403 Chain C: R.407 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: R.142, H.143 Chain D: R.142, H.143 Ligands: GOL.1, GOL.27, GOL.31 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain B: W.399, E.403, R.407 Ligands: GOL.11 Ligand excluded by PLIP GOL.10: 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.11: 6 residues within 4Å: Chain A: R.407 Chain B: S.398, W.399, T.400, E.403 Ligands: GOL.9 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain B: R.142, I.144, T.148 Chain C: N.174 Chain F: R.142 Ligands: GOL.48 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: E.217, A.220, G.221, K.222, D.314 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: N.174 Chain C: R.142, I.144, T.148, R.173 Chain E: R.142 Ligands: GOL.22 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain C: W.399, E.403, R.407 Ligands: GOL.20 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain C: L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: R.407 Chain C: L.397, S.398, W.399, T.400, E.403 Ligands: GOL.18 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain C: H.211, G.366, G.432, I.433, L.434, P.435 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain C: R.142, H.143 Chain E: R.142, H.143 Ligands: GOL.17, GOL.38 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain C: S.251, D.252, S.253, G.255, G.303, Q.304, R.305 Ligands: A2R.25 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain C: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain A: R.142 Chain D: R.142, I.144, T.148 Chain E: N.174 Ligands: GOL.5, GOL.31 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain D: W.399, E.403, R.407 Ligand excluded by PLIP GOL.29: 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.30: 5 residues within 4Å: Chain D: L.397, S.398, W.399, E.403 Chain F: R.407 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain A: R.142, H.143 Chain D: R.142, H.143 Ligands: GOL.1, GOL.5, GOL.27 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain D: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain E: W.399, E.403, R.407 Ligands: GOL.37 Ligand excluded by PLIP GOL.36: 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.37: 6 residues within 4Å: Chain D: R.407 Chain E: S.398, W.399, T.400, E.403 Ligands: GOL.35 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain C: R.142 Chain E: R.142, I.144, T.148 Chain F: N.174 Ligands: GOL.22 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain E: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain E: E.217, A.220, G.221, K.222, D.314 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain B: R.142 Chain D: N.174 Chain F: R.142, I.144, T.148, R.173 Ligands: GOL.48 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain F: W.399, E.403, R.407 Ligands: GOL.46 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain F: L.105, G.107, S.414, C.415, N.418, K.448 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain E: R.407 Chain F: L.397, S.398, W.399, T.400, E.403 Ligands: GOL.44 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain F: H.211, G.366, G.432, I.433, L.434, P.435 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain B: R.142, H.143 Chain F: R.142, H.143 Ligands: GOL.12, GOL.43 Ligand excluded by PLIP GOL.49: 8 residues within 4Å: Chain F: S.251, D.252, S.253, G.255, G.303, Q.304, R.305 Ligands: A2R.51 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain F: Q.12, N.323, T.350, Q.351 Ligand excluded by PLIP

6 x SIN: SUCCINIC ACID(Non-covalent)

SIN.6: 13 residues within 4Å: Chain A: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, T.181, R.193, N.379, G.382, V.383, S.386 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.152, A:V.383 Hydrogen bonds: A:G.80, A:Q.99, A:T.181, A:S.386 Water bridges: A:K.102, A:D.154, A:D.154, A:N.379 Salt bridges: A:K.78, A:K.102, A:K.114, A:R.193 SIN.13: 14 residues within 4Å: Chain B: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, T.181, R.193, N.379, G.382, V.383, S.386 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.152, B:V.383 Hydrogen bonds: B:G.80, B:Q.99, B:T.181, B:N.379, B:S.386 Water bridges: B:K.114, B:D.154, B:D.154, B:N.379 Salt bridges: B:K.78, B:K.102, B:K.114, B:R.193 SIN.24: 13 residues within 4Å: Chain C: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, T.181, R.193, N.379, G.382, V.383, S.386 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.152, C:V.383 Hydrogen bonds: C:G.80, C:Q.99, C:T.181, C:G.382, C:S.386 Water bridges: C:K.102, C:K.114, C:N.379 Salt bridges: C:K.78, C:K.102, C:K.114, C:R.193 SIN.32: 13 residues within 4Å: Chain D: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, T.181, R.193, N.379, G.382, V.383, S.386 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:A.152, D:V.383 Hydrogen bonds: D:G.80, D:Q.99, D:T.181, D:S.386 Water bridges: D:K.102, D:D.154, D:D.154, D:N.379 Salt bridges: D:K.78, D:K.102, D:K.114, D:R.193 SIN.39: 14 residues within 4Å: Chain E: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, G.153, T.181, R.193, N.379, G.382, V.383, S.386 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:A.152, E:V.383 Hydrogen bonds: E:G.80, E:Q.99, E:T.181, E:N.379, E:S.386 Water bridges: E:K.114, E:D.154, E:D.154, E:N.379 Salt bridges: E:K.78, E:K.102, E:K.114, E:R.193 SIN.50: 13 residues within 4Å: Chain F: K.78, G.79, G.80, Q.99, K.102, K.114, A.152, T.181, R.193, N.379, G.382, V.383, S.386 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:A.152, F:V.383 Hydrogen bonds: F:G.80, F:Q.99, F:T.181, F:G.382, F:S.386 Water bridges: F:K.102, F:K.114, F:N.379 Salt bridges: F:K.78, F:K.102, F:K.114, F:R.193

6 x A2R: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

A2R.7: 23 residues within 4Å: Chain A: R.82, H.84, K.122, D.154, I.155, G.156, 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 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:R.82, A:H.84, A:D.154, A:D.154, A:G.156, A:S.229, A:S.229, A:N.231, A:V.232, A:S.253, A:Q.284, A:Q.284, A:A.320, A:T.321, A:N.346, A:N.346, A:N.379 Water bridges: A:R.82, A:K.122, A:K.122, A:D.154, A:D.154, A:D.154, A:G.230, A:A.233, A:S.253, A:K.279, A:K.279 Salt bridges: A:K.122, A:K.279 A2R.14: 23 residues within 4Å: Chain B: R.82, H.84, K.122, D.154, I.155, G.156, 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 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:R.82, B:H.84, B:D.154, B:D.154, B:G.156, B:S.229, B:S.229, B:N.231, B:V.232, B:S.253, B:Q.284, B:Q.284, B:A.320, B:T.321, B:N.346, B:N.346, B:N.379 Water bridges: B:R.82, B:K.122, B:D.154, B:D.154, B:D.154, B:D.154, B:G.230, B:A.233, B:K.279, B:K.279 Salt bridges: B:K.122, B:K.279 A2R.25: 24 residues within 4Å: Chain C: R.82, H.84, K.122, D.154, I.155, G.156, 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.23 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:R.82, C:H.84, C:D.154, C:D.154, C:G.156, C:S.229, C:S.229, C:N.231, C:V.232, C:S.253, C:Q.284, C:Q.284, C:A.320, C:N.346, C:N.346, C:N.379 Water bridges: C:R.82, C:K.114, C:D.154, C:G.230, C:A.233, C:K.279, C:K.279 Salt bridges: C:K.122, C:K.279 A2R.33: 23 residues within 4Å: Chain D: R.82, H.84, K.122, D.154, I.155, G.156, 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 30 PLIP interactions: 30 interactions with chain D Hydrogen bonds: D:R.82, D:H.84, D:D.154, D:D.154, D:G.156, D:S.229, D:S.229, D:N.231, D:V.232, D:S.253, D:Q.284, D:Q.284, D:A.320, D:T.321, D:N.346, D:N.346, D:N.379 Water bridges: D:R.82, D:K.122, D:K.122, D:D.154, D:D.154, D:D.154, D:G.230, D:A.233, D:S.253, D:K.279, D:K.279 Salt bridges: D:K.122, D:K.279 A2R.40: 23 residues within 4Å: Chain E: R.82, H.84, K.122, D.154, I.155, G.156, 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 29 PLIP interactions: 29 interactions with chain E Hydrogen bonds: E:R.82, E:H.84, E:D.154, E:D.154, E:G.156, E:S.229, E:S.229, E:N.231, E:V.232, E:S.253, E:Q.284, E:Q.284, E:A.320, E:T.321, E:N.346, E:N.346, E:N.379 Water bridges: E:R.82, E:K.122, E:D.154, E:D.154, E:D.154, E:D.154, E:G.230, E:A.233, E:K.279, E:K.279 Salt bridges: E:K.122, E:K.279 A2R.51: 24 residues within 4Å: Chain F: R.82, H.84, K.122, D.154, I.155, G.156, 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.49 25 PLIP interactions: 25 interactions with chain F Hydrogen bonds: F:R.82, F:H.84, F:D.154, F:D.154, F:G.156, F:S.229, F:S.229, F:N.231, F:V.232, F:S.253, F:Q.284, F:Q.284, F:A.320, F:N.346, F:N.346, F:N.379 Water bridges: F:R.82, F:K.114, F:D.154, F:G.230, F:A.233, F:K.279, 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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