- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.74 Å
- Oligo State
- homo-hexamer
- Ligands
- 48 x GOL: GLYCEROL(Non-functional Binders)
- 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
AB
BC
CD
AE
BF
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.74 Å
- Oligo State
- homo-hexamer
- Ligands
- 48 x GOL: GLYCEROL(Non-functional Binders)
- 12 x MLI: MALONATE ION(Non-functional Binders)
- 6 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(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