- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.24 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)
AKG.3: 7 residues within 4Å:- Chain A: R.60, S.61, C.83, I.84, G.85, N.108
- Chain B: K.141
11 PLIP interactions:9 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:S.61, A:I.84, A:G.85
- Water bridges: A:R.60, A:R.60, A:R.60, A:R.60, A:R.60
- Salt bridges: A:R.60, B:K.141, B:K.141
AKG.8: 8 residues within 4Å:- Chain A: K.141
- Chain B: R.60, S.61, C.83, I.84, N.108, S.296, I.304
8 PLIP interactions:1 interactions with chain A, 7 interactions with chain B- Salt bridges: A:K.141, B:R.60
- Hydrogen bonds: B:S.61, B:I.84, B:N.108
- Water bridges: B:R.60, B:R.60, B:G.85
AKG.12: 7 residues within 4Å:- Chain C: R.60, S.61, C.83, I.84, N.108, I.304
- Chain D: K.141
9 PLIP interactions:8 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:S.61, C:I.84, C:N.108
- Water bridges: C:R.60, C:R.60, C:G.85, C:G.295
- Salt bridges: C:R.60, D:K.141
AKG.17: 6 residues within 4Å:- Chain C: K.141
- Chain D: R.60, S.61, C.83, N.108
- Ligands: NAD.20
11 PLIP interactions:9 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:S.61, D:N.108
- Water bridges: D:R.60, D:R.60, D:S.61, D:G.295, D:Q.301, C:K.141
- Salt bridges: D:R.60, D:H.292, C:K.141
- 7 x UNL: UNKNOWN LIGAND(Non-functional Binders)(Non-covalent)
UNL.4: 5 residues within 4Å:- Chain A: Y.180, Q.195, H.196, L.197, S.198
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:Y.180
- Hydrogen bonds: A:Q.195, A:L.197, A:S.198
- Water bridges: A:E.225
- Salt bridges: A:H.196
UNL.5: 5 residues within 4Å:- Chain A: H.38, K.39, G.40, A.41, L.42
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:H.38
- Hydrogen bonds: A:H.38, A:K.39, A:G.40
- Salt bridges: A:K.39
UNL.9: 4 residues within 4Å:- Chain B: Y.180, H.196, L.197, S.198
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:Y.180, B:H.196, B:L.197, B:S.198, B:S.198
- Salt bridges: B:H.196
UNL.13: 5 residues within 4Å:- Chain C: Y.180, Q.195, H.196, L.197, S.198
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:Y.180, C:L.197
- Hydrogen bonds: C:Y.180, C:H.196, C:L.197, C:S.198
- Salt bridges: C:H.196
UNL.14: 3 residues within 4Å:- Chain C: H.38, K.39, G.40
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:K.39, C:G.40
- Salt bridges: C:H.38, C:K.39
UNL.18: 4 residues within 4Å:- Chain D: Y.180, H.196, L.197, S.198
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:Y.180, D:L.197
- Hydrogen bonds: D:Y.180, D:L.197, D:S.198
- Salt bridges: D:H.196
UNL.19: 6 residues within 4Å:- Chain D: H.38, K.39, G.40, A.41, L.42, Q.46
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:H.38, D:K.39, D:G.40, D:Q.46
- Salt bridges: D:H.38, D:H.38, D:K.39
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.6: 28 residues within 4Å:- Chain A: I.84, F.106, N.108, V.112, I.157, G.158, Y.159, G.160, H.161, I.162, Y.180, D.181, I.182, K.185, H.210, V.211, P.212, S.216, T.217, M.220, A.238, S.239, R.240, D.264, V.265, H.292, G.294, G.295
21 PLIP interactions:21 interactions with chain A- Hydrophobic interactions: A:I.84, A:N.108, A:V.112
- Hydrogen bonds: A:Y.159, A:H.161, A:I.162, A:I.182, A:K.185, A:K.185, A:V.211, A:S.216, A:S.216, A:R.240, A:D.264, A:G.294, A:G.295
- Water bridges: A:G.160, A:G.163, A:Y.180, A:R.240
- Salt bridges: A:H.161
NAD.10: 28 residues within 4Å:- Chain B: I.84, F.106, N.108, V.112, I.157, G.158, Y.159, G.160, H.161, I.162, Y.180, D.181, I.182, K.185, H.210, V.211, P.212, S.216, T.217, M.220, A.238, S.239, R.240, D.264, V.265, H.292, G.294, G.295
22 PLIP interactions:22 interactions with chain B- Hydrophobic interactions: B:I.84, B:N.108, B:V.112
- Hydrogen bonds: B:Y.159, B:Y.159, B:H.161, B:I.162, B:I.182, B:K.185, B:K.185, B:V.211, B:S.216, B:S.216, B:R.240, B:D.264, B:D.264, B:G.294, B:G.295
- Water bridges: B:G.160, B:H.161, B:G.163, B:R.240
NAD.15: 28 residues within 4Å:- Chain C: I.84, F.106, N.108, V.112, I.157, G.158, Y.159, G.160, H.161, I.162, Y.180, D.181, I.182, E.183, K.185, H.210, V.211, P.212, S.216, T.217, A.238, S.239, R.240, D.264, V.265, H.292, G.294, G.295
20 PLIP interactions:20 interactions with chain C- Hydrophobic interactions: C:I.84, C:N.108, C:V.112
- Hydrogen bonds: C:Y.159, C:Y.159, C:H.161, C:I.162, C:I.182, C:K.185, C:V.211, C:S.216, C:S.216, C:R.240, C:D.264, C:D.264, C:G.295
- Water bridges: C:G.160, C:G.163, C:N.214
- Salt bridges: C:H.161
NAD.20: 27 residues within 4Å:- Chain D: F.106, N.108, V.112, G.158, Y.159, G.160, H.161, I.162, Y.180, D.181, I.182, E.183, K.185, H.210, V.211, P.212, S.216, T.217, M.220, A.238, S.239, R.240, D.264, H.292, G.294, G.295
- Ligands: AKG.17
22 PLIP interactions:22 interactions with chain D- Hydrophobic interactions: D:V.112, D:I.162
- Hydrogen bonds: D:Y.159, D:Y.159, D:H.161, D:I.162, D:I.182, D:E.183, D:E.183, D:K.185, D:V.211, D:S.216, D:S.216, D:R.240, D:D.264, D:G.294, D:G.295
- Water bridges: D:G.160, D:G.163, D:N.214, D:R.240
- Salt bridges: D:H.161
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Thompson, J.R. et al., Vmax Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase. Biochemistry (2005)
- Release Date
- 2005-04-26
- Peptides
- D-3-phosphoglycerate dehydrogenase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.24 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)
- 7 x UNL: UNKNOWN LIGAND(Non-functional Binders)(Non-covalent)
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Thompson, J.R. et al., Vmax Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase. Biochemistry (2005)
- Release Date
- 2005-04-26
- Peptides
- D-3-phosphoglycerate dehydrogenase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D