- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.73 Å
- Oligo State
- homo-hexamer
- Ligands
- 40 x GOL: GLYCEROL(Non-functional Binders)
- 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
AB
BC
CD
AE
BF
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.73 Å
- Oligo State
- homo-hexamer
- Ligands
- 40 x GOL: GLYCEROL(Non-functional Binders)
- 6 x SIN: SUCCINIC ACID(Non-covalent)
- 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)
- 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
AB
BC
CD
AE
BF
C