SMTL ID : 2p9c.1

Crystal structure of serine bound G336V mutant of E.coli phosphoglycerate dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 27 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, H.292, G.294, G.295 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.84, A:N.108, A:V.112, A:I.162 Hydrogen bonds: A:Y.159, A:H.161, A:I.162, A:I.182, A:K.185, A:V.211, A:S.216, A:D.264, A:D.264, A:G.294, A:G.295 Water bridges: A:G.160 Salt bridges: A:H.161 NAI.4: 26 residues within 4Å: Chain B: 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, M.220, A.238, S.239, R.240, D.264, H.292, G.294, G.295 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.84, B:V.112, B:I.162 Hydrogen bonds: B:Y.159, B:H.161, B:I.162, B:I.182, B:E.183, B:E.183, B:K.185, B:V.211, B:S.216, B:R.240, B:D.264, B:G.295 Salt bridges: B:H.161, B:H.161 NAI.5: 27 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, 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 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.84, C:N.108, C:V.112, C:I.162 Hydrogen bonds: C:Y.159, C:H.161, C:I.162, C:I.182, C:K.185, C:V.211, C:S.216, C:D.264, C:D.264, C:G.294, C:G.295 Water bridges: C:G.160 Salt bridges: C:H.161 NAI.8: 26 residues within 4Å: Chain D: 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, M.220, A.238, S.239, R.240, D.264, H.292, G.294, G.295 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.84, D:V.112, D:I.162 Hydrogen bonds: 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:R.240, D:D.264, D:G.295 Salt bridges: D:H.161, D:H.161

4 x SER: SERINE(Non-covalent)

SER.2: 11 residues within 4Å: Chain A: H.344, E.345, N.346, R.347, P.348, G.349, L.351, L.370, T.372 Chain D: N.364, I.365 8 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.346, A:N.346, A:R.347, A:G.349, D:N.364, D:I.365, S.2 Salt bridges: A:H.344 SER.3: 11 residues within 4Å: Chain B: H.344, E.345, N.346, R.347, P.348, G.349, V.350, L.351, L.370 Chain C: N.364, I.365 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.346, B:R.347, B:G.349, C:N.364, C:I.365 Salt bridges: B:H.344 SER.6: 11 residues within 4Å: Chain B: N.364, I.365 Chain C: H.344, E.345, N.346, R.347, P.348, G.349, L.351, L.370, T.372 8 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.346, C:N.346, C:R.347, C:G.349, B:N.364, B:I.365, S.6 Salt bridges: C:H.344 SER.7: 11 residues within 4Å: Chain A: N.364, I.365 Chain D: H.344, E.345, N.346, R.347, P.348, G.349, V.350, L.351, L.370 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.346, D:R.347, D:G.349, A:N.364, A:I.365 Salt bridges: D:H.344

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
A

D
B

D-3-phosphoglycerate dehydrogenase

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