SMTL ID : 1z82.1

Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from THERMOTOGA MARITIMA at 2.00 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 25 residues within 4Å: Chain A: A.22, G.23, S.24, W.25, G.26, R.45, R.46, Y.61, A.87, P.89, Y.92, E.95, H.96, L.110, S.111, K.112, S.141, H.142, A.143, R.255, N.277, Q.278, V.279, E.281 Ligands: G3P.8 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:W.25, A:W.25 Hydrogen bonds: A:A.22, A:S.24, A:W.25, A:G.26, A:Y.61, A:Y.61, A:E.95, A:S.111, A:K.112, A:A.143, A:E.144, A:V.279 Water bridges: A:A.22, A:G.23, A:S.24, A:R.46, A:R.46, A:N.192, A:R.255, A:R.255, A:E.281 Salt bridges: A:R.45, A:R.46, A:R.255, A:R.255 pi-Stacking: A:Y.92 pi-Cation interactions: A:R.45, A:R.45 NDP.7: 27 residues within 4Å: Chain B: A.22, G.23, S.24, W.25, G.26, R.45, R.46, Y.61, A.87, I.88, P.89, Y.92, E.95, H.96, L.110, S.111, K.112, S.141, H.142, A.143, E.144, R.255, N.277, Q.278, V.279, E.281 Ligands: G3H.2 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:W.25, B:W.25 Hydrogen bonds: B:A.22, B:S.24, B:W.25, B:G.26, B:Y.61, B:E.95, B:S.111, B:K.112, B:K.112, B:S.141, B:A.143, B:V.279, B:E.281 Water bridges: B:A.22, B:G.23, B:S.24, B:R.46, B:R.99, B:H.142, B:N.192, B:R.255, B:R.255 Salt bridges: B:R.45, B:R.46, B:R.255, B:R.255 pi-Stacking: B:Y.92 pi-Cation interactions: B:R.45, B:R.45

1 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Non-covalent)

G3H.2: 15 residues within 4Å: Chain B: K.112, G.139, P.140, S.141, H.142, K.191, N.192, D.244, V.247, T.248, Y.253, S.254, R.255, N.256 Ligands: NDP.7 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.112, B:S.141, B:K.191, B:N.192, B:R.255, B:N.256, B:N.256 Water bridges: B:H.142, B:Y.253, B:R.255 Salt bridges: B:H.142, B:K.191, B:R.255

5 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 10 residues within 4Å: Chain A: A.197, I.200, L.201, L.214, E.305, V.306, V.309, S.319, M.320, L.323 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.197, A:I.200, A:I.200, A:L.201, A:L.214, A:E.305, A:V.309 Hydrogen bonds: A:S.319 MRD.9: 10 residues within 4Å: Chain B: A.197, I.200, L.201, F.204, E.305, V.306, S.319, M.320, L.323 Ligands: MRD.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.197, B:I.200, B:I.200, B:L.201, B:L.201, B:F.204, B:E.305, B:V.306 Hydrogen bonds: B:S.319 MRD.10: 7 residues within 4Å: Chain A: P.151, T.152, A.153 Chain B: A.210, A.213, M.324 Ligands: MRD.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.151, B:A.213 Water bridges: A:Y.176 MRD.11: 9 residues within 4Å: Chain B: R.255, R.258, F.259, L.262, L.272, S.275, S.276, Q.278, V.280 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.255, B:F.259, B:L.262, B:Q.278, B:V.280 MRD.12: 3 residues within 4Å: Chain B: M.15, E.163, R.167 No protein-ligand interaction detected (PLIP)

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 8 residues within 4Å: Chain A: A.210, A.213, L.214, R.217, M.320, L.323, M.324 Chain B: P.151 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.151, A:A.213 Hydrogen bonds: A:R.217 MPD.5: 8 residues within 4Å: Chain A: R.255, R.258, L.262, L.272, S.275, S.276, Q.278, V.280 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.255, A:L.262, A:L.272, A:Q.278 Water bridges: A:R.258 MPD.6: 2 residues within 4Å: Chain A: G.266, F.267 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.267, A:F.267

1 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.8: 15 residues within 4Å: Chain A: K.112, G.139, P.140, S.141, H.142, K.191, N.192, D.244, V.247, T.248, Y.253, S.254, R.255, N.256 Ligands: NDP.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.112, A:G.139, A:S.141, A:K.191, A:Y.253, A:R.255, A:N.256, A:N.256 Water bridges: A:K.191, A:N.192 Salt bridges: A:H.142, A:K.191, A:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from Thermotoga maritima at 2.00 A resolution. To be Published

Release Date

2005-04-12

Peptides

glycerol-3-phosphate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

glycerol-3-phosphate dehydrogenase