SMTL ID : 1yba.1

The active form of phosphoglycerate dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-tetramer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: L.142, A.143, A.144 Chain B: R.60 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.143, A:A.144 Water bridges: B:R.60 Salt bridges: B:R.60 PO4.2: 5 residues within 4Å: Chain A: I.84, G.85, T.86, N.87, R.240 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.86, A:N.87 Water bridges: A:N.87, A:N.87, A:Q.88, A:R.240 Salt bridges: A:R.240 PO4.7: 4 residues within 4Å: Chain A: R.60 Chain B: L.142, A.143, A.144 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:E.17, A:R.60, A:R.60, A:R.60, A:Q.301 Salt bridges: A:R.60 Hydrogen bonds: B:A.143, B:A.144 PO4.11: 4 residues within 4Å: Chain C: L.142, A.143, A.144 Chain D: R.60 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Water bridges: D:G.18, D:R.60, D:R.60 Salt bridges: D:R.60 Hydrogen bonds: C:A.143, C:A.144 PO4.16: 4 residues within 4Å: Chain C: R.60 Chain D: L.142, A.143, A.144 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:R.60, C:Q.301 Salt bridges: C:R.60 Hydrogen bonds: D:A.143, D:A.144

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
A

B
B

C
C

D
D

D-3-phosphoglycerate dehydrogenase