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

Crystal structure of Glycerol-3-phosphate Dehydrogenase from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

BOG.1: 8 residues within 4Å: Chain A: P.97, A.98, W.99, R.102, I.103, R.137 Ligands: BOG.2, EDO.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.103 Hydrogen bonds: A:A.98, A:W.99, A:R.137 BOG.2: 4 residues within 4Å: Chain A: R.102, T.121, G.122 Ligands: BOG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.102 Salt bridges: A:R.102

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

SO4.3: 5 residues within 4Å: Chain A: V.310, W.311, W.468, G.474, M.475 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.475 SO4.4: 5 residues within 4Å: Chain A: Y.398, R.401, L.402, R.405, E.426 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.426

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

PO4.5: 5 residues within 4Å: Chain A: R.54, Y.55, R.317, R.332, K.354 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.55, A:Y.55 Water bridges: A:Y.55, A:Y.55, A:R.332 Salt bridges: A:R.54, A:R.317, A:R.332, A:K.354

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

FAD.6: 39 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, F.213, G.231, H.233, T.270, G.315, V.316, R.317, G.353, K.354, L.355, T.356 Ligands: EDO.9 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:T.41, A:T.270, A:R.317 Hydrogen bonds: A:G.11, A:G.12, A:N.14, A:N.14, A:A.34, A:T.41, A:T.41, A:S.42, A:S.42, A:S.46, A:L.48, A:L.48, A:A.172, A:A.172, A:K.354, A:L.355, A:T.356, A:T.356 Water bridges: A:G.15, A:A.40, A:A.40, A:S.46, A:Y.55, A:G.207 pi-Cation interactions: A:K.354

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

EDO.7: 4 residues within 4Å: Chain A: R.254, T.271, D.272, Y.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.272 Water bridges: A:D.252 EDO.8: 4 residues within 4Å: Chain A: L.293, N.294, N.297, T.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.294, A:N.297, A:T.298 Water bridges: A:N.294 EDO.9: 5 residues within 4Å: Chain A: A.34, C.39, W.209, K.280 Ligands: FAD.6 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: W.311, W.468 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: W.145, W.261, M.262, R.419 Ligands: EDO.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.262, A:R.419 Water bridges: A:D.263 EDO.12: 2 residues within 4Å: Chain A: I.289, R.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.306 Water bridges: A:I.309 EDO.14: 7 residues within 4Å: Chain A: S.43, A.44, W.311, Y.313, S.314, W.468 Ligands: EDO.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.314, A:W.468 Water bridges: A:S.43, A:S.43, A:K.47, A:K.47, A:S.314 EDO.15: 6 residues within 4Å: Chain A: R.88, R.124, F.125, S.129, V.130, Q.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.88, A:V.130, A:Q.242 EDO.16: 6 residues within 4Å: Chain A: P.208, W.209, Q.212, L.228, G.277, P.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.208 EDO.17: 5 residues within 4Å: Chain A: V.455, D.456, H.457, E.458, W.459 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.459 EDO.18: 1 residues within 4Å: Chain A: E.448 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain A: L.53, R.96, I.101, I.255 No protein-ligand interaction detected (PLIP) EDO.20: 6 residues within 4Å: Chain A: M.262, H.416, T.420, Q.473 Ligands: EDO.11, EDO.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.416, A:Q.473 Water bridges: A:D.147, A:K.472, A:K.472 EDO.21: 5 residues within 4Å: Chain A: H.416, H.444, E.445, Q.473 Ligands: EDO.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.445, A:Q.473 Water bridges: A:H.416 EDO.22: 5 residues within 4Å: Chain A: H.91, P.93, P.97, A.98 Ligands: BOG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.98

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.13: 7 residues within 4Å: Chain A: Q.157, V.160, R.161, P.387, N.424, L.427, H.457 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.157 Hydrogen bonds: A:Q.157, A:Q.157, A:R.161, A:N.424 Water bridges: A:G.388

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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