SMTL ID : 2p9e.1

Crystal Structure of G336V mutant of E.coli phosphoglycerate dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

8 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.143, A:A.144 Salt bridges: B:R.60 PO4.2: 5 residues within 4Å: Chain A: I.84, G.85, T.86, N.87, R.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.86, A:N.87, A:N.87 Salt bridges: A:R.240 PO4.6: 3 residues within 4Å: Chain B: H.196, L.197, S.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.197, B:S.198 Salt bridges: B:H.196 PO4.7: 4 residues within 4Å: Chain A: R.60 Chain B: L.142, A.143, A.144 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.143, B:A.144 Salt bridges: A:R.60 PO4.10: 4 residues within 4Å: Chain C: R.60 Chain D: L.142, A.143, A.144 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:A.143, D:A.144 Water bridges: C:Q.298 Salt bridges: C:R.60 PO4.11: 4 residues within 4Å: Chain C: L.142, A.143, A.144 Chain D: R.60 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.60 Hydrogen bonds: C:A.143, C:A.144 PO4.16: 4 residues within 4Å: Chain C: K.141 Chain D: R.60, S.61, A.83 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.61, D:S.61, D:S.61 Salt bridges: D:R.60, C:K.141 PO4.17: 3 residues within 4Å: Chain D: H.38, K.39, G.40 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.38, D:K.39, D:G.40 Salt bridges: D:H.38

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 27 residues within 4Å: Chain A: I.84, F.106, 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, V.265, H.292, G.294, G.295 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.84, A:V.112 Hydrogen bonds: A:Y.159, A:H.161, A:I.162, A:I.182, A:E.183, A:K.185, A:V.211, A:S.216, A:S.216, A:S.239, A:R.240, A:G.295 Salt bridges: A:H.161 NAI.8: 27 residues within 4Å: Chain B: I.84, F.106, N.108, V.112, G.158, Y.159, G.160, H.161, I.162, 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, V.265, H.292, G.294, G.295 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.84, B:N.108, B:V.112, B:I.162 Hydrogen bonds: B:Y.159, B:H.161, B:I.162, B:I.182, B:E.183, B:V.211, B:N.214, B:S.216, B:S.216, B:R.240, B:D.264, B:G.294, B:G.295 Salt bridges: B:H.161 NAI.13: 25 residues within 4Å: Chain C: I.84, F.106, N.108, V.112, 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, A.238, S.239, R.240, D.264, H.292, G.294, G.295 19 PLIP interactions: 19 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: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.294, C:G.295 Salt bridges: C:H.161 NAI.18: 24 residues within 4Å: Chain D: N.108, V.112, 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, M.220, A.238, S.239, R.240, D.264, V.265, H.292, G.294, G.295 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:V.112 Hydrogen bonds: D:Y.159, D:Y.159, D:H.161, D:H.161, D:I.162, D:I.182, D:K.185, D:K.185, D:V.211, D:S.216, D:S.216, D:D.264, D:G.294, D:G.295 Salt bridges: D:H.161

6 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 5 residues within 4Å: Chain A: Y.180, Q.195, H.196, L.197, S.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.197, A:S.198, A:S.198 Salt bridges: A:H.196, A:H.196 CIT.5: 6 residues within 4Å: Chain A: F.37, H.38, K.39, G.40, A.41, L.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.39, A:G.40 Salt bridges: A:H.38, A:H.38 CIT.9: 10 residues within 4Å: Chain A: K.141 Chain B: R.60, S.61, A.83, I.84, G.85, N.108, S.296, Q.301, I.304 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.83 Hydrogen bonds: B:S.61, B:S.61, B:I.84, B:G.85, B:N.108, B:Q.301, A:K.141, A:K.141 Salt bridges: B:R.60, A:K.141 CIT.14: 6 residues within 4Å: Chain C: Y.180, Q.195, H.196, L.197, S.198, K.224 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.180, C:H.196, C:L.197, C:S.198, C:S.198 Salt bridges: C:H.196, C:K.224 CIT.15: 7 residues within 4Å: Chain C: R.60, S.61, A.83, I.84, G.85, N.108 Chain D: K.141 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.61, C:I.84, C:G.85, C:N.108, C:N.108, D:K.141 Salt bridges: C:R.60 CIT.19: 5 residues within 4Å: Chain D: Y.180, H.196, L.197, S.198, E.225 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.180, D:L.197, D:S.198 Salt bridges: D:H.196, D:H.196

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 3 residues within 4Å: Chain C: H.38, K.39, G.40 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.39, C:G.40 Salt bridges: C:H.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dey, S. et al., The Effect of Hinge Mutations on Effector Binding and Domain Rotation in Escherichia coli D-3-Phosphoglycerate Dehydrogenase. J.Biol.Chem. (2007)

Release Date

2007-04-24

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

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