SMTL ID : 2r45.2 (1 other biounit)

Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with 2-phospho-d-glyceric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 4 residues within 4Å: Chain A: A.98, W.99, R.102, R.137 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.102 Hydrogen bonds: A:R.102, A:R.137 Salt bridges: A:R.102 BOG.2: 10 residues within 4Å: Chain A: L.53, R.54, L.56, E.57, L.89, R.96, M.100, I.101, G.104, L.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.57, A:E.57, A:I.101, A:L.105 Water bridges: A:E.57

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

PO4.3: 4 residues within 4Å: Chain A: Y.398, R.401, L.402, R.405 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.398 Salt bridges: A:R.401, A:R.405 PO4.4: 5 residues within 4Å: Chain A: P.208, Q.212, L.228, G.277, P.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.208, A:P.208 Water bridges: A:G.277 PO4.5: 3 residues within 4Å: Chain A: R.462, A.463, D.464 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.462, A:D.464, A:D.464, A:D.464 Water bridges: A:A.463, A:A.463 PO4.6: 3 residues within 4Å: Chain A: R.92, P.93, H.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.94 Salt bridges: A:H.94

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.7: 38 residues within 4Å: Chain A: I.9, G.10, G.11, G.12, I.13, N.14, L.32, E.33, A.34, C.39, A.40, T.41, S.42, A.44, S.45, S.46, K.47, L.48, H.50, T.170, R.171, A.172, A.205, T.206, G.207, P.208, W.209, G.231, H.233, T.270, G.315, V.316, R.317, G.353, K.354, L.355, T.356 Ligands: EDO.9 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.41, A:R.317 Hydrogen bonds: A:G.12, A:N.14, A:N.14, A:G.15, A:A.34, A:T.41, A:S.42, A:S.42, A:S.46, A:L.48, A:L.48, A:H.50, A:A.172, A:A.172, A:K.354, A:L.355, A:T.356 Water bridges: A:A.40, A:S.46, A:S.46, A:G.207 pi-Cation interactions: A:K.354

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: R.254, T.271, D.272, Y.291, Q.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.272 EDO.9: 4 residues within 4Å: Chain A: A.34, R.171, W.209 Ligands: FAD.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.209 EDO.10: 3 residues within 4Å: Chain A: W.311, W.468 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.311 EDO.11: 5 residues within 4Å: Chain A: S.43, W.311, W.468, R.469 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.43, A:R.469 Water bridges: A:S.43, A:K.472 EDO.12: 5 residues within 4Å: Chain A: S.412, H.416, H.444, E.445, Q.473 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.416, A:H.444, A:H.444, A:Q.473 Water bridges: A:H.416 EDO.13: 5 residues within 4Å: Chain A: M.158, R.161, K.162, S.384, V.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.161, A:K.162 EDO.14: 2 residues within 4Å: Chain A: V.310, W.311 No protein-ligand interaction detected (PLIP) EDO.17: 5 residues within 4Å: Chain A: Q.157, R.161, P.387, N.424 Ligands: T3A.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.157, A:N.424, A:N.424

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.15: 4 residues within 4Å: Chain A: E.448, W.488, E.491, Y.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.491

1 x T3A: N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC ACID(Non-covalent)

T3A.16: 8 residues within 4Å: Chain A: Q.157, V.160, V.455, D.456, H.457, E.458, W.459 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.459

1 x 2PG: 2-PHOSPHOGLYCERIC ACID(Non-covalent)

2PG.18: 10 residues within 4Å: Chain A: R.54, Y.55, R.254, I.255, F.257, T.270, D.272, R.317, R.332, K.354 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.55, A:I.255, A:T.270 Water bridges: A:S.46, A:R.54, A:Y.55 Salt bridges: A:R.54, A:R.254, A:R.317, A:R.332, A:K.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeh, J.I. et al., Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-04-15

Peptides

Aerobic glycerol-3-phosphate dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Aerobic glycerol-3-phosphate dehydrogenase

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