SMTL ID : 2r4e.2 (1 other biounit)

Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

BOG.1: 5 residues within 4Å: Chain A: A.98, W.99, R.102, I.103, R.137 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.103 Hydrogen bonds: A:W.99, A:R.102, A:R.102, A:R.137 Salt bridges: A:R.102 BOG.2: 11 residues within 4Å: Chain A: L.53, R.54, L.56, E.57, Y.59, F.61, L.89, R.96, I.101, G.104, L.105 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.56, A:Y.59, A:F.61 Hydrogen bonds: A:E.57, A:I.101, A:L.105

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

PO4.3: 4 residues within 4Å: Chain A: Y.398, R.401, L.402, R.405 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.398, A:Y.398, A:Y.398 Salt bridges: A:R.401, A:R.405 PO4.4: 6 residues within 4Å: Chain A: P.208, W.209, Q.212, L.228, G.277, P.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.208 Water bridges: A:Q.212 PO4.5: 4 residues within 4Å: Chain A: H.91, R.92, P.93, H.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.91, A:R.92, A:H.94 Salt bridges: A:H.94

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

FAD.6: 38 residues within 4Å: Chain A: I.9, G.10, G.11, G.12, I.13, N.14, L.32, E.33, A.34, Q.35, 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, V.316, R.317, G.353, K.354, L.355, T.356 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:Q.35, A:A.40, 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:S.46, A:S.46, A:Y.55, A:G.207 pi-Cation interactions: A:K.354

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

EDO.7: 3 residues within 4Å: Chain A: R.254, T.271, D.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.272 Water bridges: A:D.252, A:D.252 EDO.8: 3 residues within 4Å: Chain A: A.34, R.171, W.209 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: W.311, W.468 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: S.43, W.311, W.468, R.469 Ligands: EDO.9 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.11: 3 residues within 4Å: Chain A: W.380, S.384, V.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.385, A:V.385 EDO.12: 3 residues within 4Å: Chain A: I.309, V.310, W.311 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.312, A:T.312 EDO.14: 5 residues within 4Å: Chain A: Q.157, R.161, P.387, N.424 Ligands: T3A.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.157, A:R.161, A:N.424

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.13: 4 residues within 4Å: Chain A: E.448, W.488, E.491, Y.492 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.491 pi-Stacking: A:W.488

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

T3A.15: 8 residues within 4Å: Chain A: Q.157, V.160, V.455, D.456, H.457, E.458, W.459 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.459 Water bridges: A:V.455, A:W.459

1 x 13P: 1,3-DIHYDROXYACETONEPHOSPHATE(Non-covalent)

13P.16: 8 residues within 4Å: Chain A: R.54, Y.55, R.254, I.255, T.270, D.272, R.317, R.332 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.254, A:R.254, A:I.255, A:G.269, A:T.270, A:T.270, A:T.270 Water bridges: A:Y.55, A:K.354 Salt bridges: A:R.54, 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

2008-04-29

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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