SMTL ID : 3cmc.1

Thioacylenzyme intermediate of Bacillus stearothermophilus phosphorylating GAPDH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: P.121, S.150, T.209, G.210, A.211 Ligands: G3H.7 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: T.181, D.183, R.196, R.232 Ligands: G3H.7, NAD.8 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: R.171 Chain B: K.304 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: R.185, P.190, H.191, K.192 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: G.61, N.62, N.63 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: G.85, A.111, G.112 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain B: P.121, S.150, T.209, G.210, A.211 Ligands: G3H.12 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain B: T.181, D.183, R.196, R.232 Ligands: G3H.12, NAD.13 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain C: P.121, S.150, T.209, G.210, A.211 Ligands: G3H.21 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain C: T.181, D.183, R.196, R.232 Ligands: G3H.21, NAD.22 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: R.185, P.190, H.191, K.192 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain D: P.121, S.150, T.209, G.210, A.211 Ligands: G3H.32 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain D: T.181, D.183, R.196, R.232 Ligands: G3H.32, NAD.33 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: D.302, K.304 Chain D: R.171 Ligand excluded by PLIP SO4.28: 1 residues within 4Å: Chain D: R.52 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain D: S.58, V.59 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain D: R.185, P.190, H.191, K.192 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: L.109, G.112, A.113, K.114 Ligand excluded by PLIP

4 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Covalent)

G3H.7: 11 residues within 4Å: Chain A: S.150, C.151, T.152, T.176, H.178, T.181, T.209, R.232 Ligands: SO4.1, SO4.2, NAD.8 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.150, A:S.150, A:C.151, A:T.152, A:T.152, A:T.209, A:R.232 Water bridges: A:R.196, A:R.196 Salt bridges: A:H.178 G3H.12: 11 residues within 4Å: Chain B: S.150, C.151, T.152, T.176, H.178, T.181, T.209, R.232 Ligands: SO4.10, SO4.11, NAD.13 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.150, B:C.151, B:T.152, B:T.152, B:T.209, B:R.232 Water bridges: B:R.196, B:R.196, B:R.196, B:R.196, B:T.209 Salt bridges: B:H.178 G3H.21: 11 residues within 4Å: Chain C: S.150, C.151, T.152, T.176, H.178, T.181, T.209, R.232 Ligands: SO4.18, SO4.19, NAD.22 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.150, C:C.151, C:T.152, C:T.152, C:T.209, C:R.232 Water bridges: C:R.196, C:R.196, C:T.209 Salt bridges: C:H.178 G3H.32: 11 residues within 4Å: Chain D: S.150, C.151, T.152, T.176, H.178, T.181, T.209, R.232 Ligands: SO4.25, SO4.26, NAD.33 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.150, D:C.151, D:T.152, D:T.152, D:T.209, D:R.232 Water bridges: D:R.196, D:R.196 Salt bridges: D:H.178

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.8: 24 residues within 4Å: Chain A: G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, C.151, N.182, N.314, Y.318 Chain D: L.189 Ligands: SO4.2, G3H.7 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.12, A:I.12, A:Y.318 Hydrogen bonds: A:F.9, A:R.11, A:I.12, A:N.32, A:R.77, A:N.182, A:N.314 Water bridges: A:N.7, A:N.7, A:G.10, A:G.13, A:R.14, A:R.77, A:G.97, A:R.98, A:S.119, A:N.182, A:N.182, A:E.315, D:L.187 NAD.13: 24 residues within 4Å: Chain B: G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, C.151, N.182, N.314, Y.318 Chain C: L.189 Ligands: SO4.11, G3H.12 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.12, B:I.12, B:Y.318 Hydrogen bonds: B:F.9, B:R.11, B:I.12, B:N.32, B:R.77, B:N.182, B:N.314 Water bridges: B:N.7, B:N.7, B:G.10, B:G.13, B:G.97, B:S.119, B:N.182, B:N.182, C:L.187 NAD.22: 24 residues within 4Å: Chain B: L.189 Chain C: G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, C.151, N.182, N.314, Y.318 Ligands: SO4.19, G3H.21 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.12, C:I.12, C:Y.318 Hydrogen bonds: C:F.9, C:R.11, C:I.12, C:N.32, C:R.77, C:N.182, C:N.314 Water bridges: C:N.7, C:N.7, C:G.10, C:G.13, C:R.14, C:R.77, C:G.97, C:S.119, C:N.182, C:N.182, C:N.182, B:L.187 NAD.33: 25 residues within 4Å: Chain A: L.189, P.190 Chain D: G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, C.151, N.182, N.314, Y.318 Ligands: SO4.26, G3H.32 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.12, D:I.12, D:Y.318 Hydrogen bonds: D:F.9, D:R.11, D:I.12, D:N.32, D:R.77, D:N.182, D:N.314 Water bridges: D:N.7, D:N.7, D:G.10, D:G.13, D:R.14, D:R.77, D:G.97, D:S.119, D:N.182, D:N.182, D:E.315, A:L.187

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: K.304 Chain B: R.171 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.304, B:R.171, B:R.171 Water bridges: A:E.246 GOL.14: 6 residues within 4Å: Chain B: G.132, V.133, N.134, Q.135, D.136, K.161 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.135, B:Q.135, B:D.136, B:D.136, B:K.161, B:K.161 GOL.15: 5 residues within 4Å: Chain B: D.183, R.185, P.190, H.191, K.192 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.183, B:R.185, B:K.192 GOL.16: 4 residues within 4Å: Chain B: K.213, A.216, K.223, G.224 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.213, B:G.224 Water bridges: B:L.222, B:K.225 GOL.17: 5 residues within 4Å: Chain B: V.49, H.50, G.51, N.285 Chain D: R.282 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:R.282, B:V.49, B:N.285 Water bridges: B:R.282, B:R.282, B:N.285 GOL.24: 5 residues within 4Å: Chain C: N.15, R.18, H.50, G.286, T.316 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.15, C:R.18, C:H.50 Water bridges: C:H.50 GOL.34: 2 residues within 4Å: Chain C: R.171 Chain D: K.304 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.304, C:R.171, C:R.171 GOL.35: 5 residues within 4Å: Chain D: V.133, N.134, Q.135, D.136, K.161 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.135, D:D.136, D:K.161

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

EDO.23: 6 residues within 4Å: Chain C: G.132, V.133, N.134, Q.135, D.136, K.161 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.135, C:Q.135, C:D.136, C:K.161 Water bridges: C:K.161, C:E.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moniot, S. et al., Trapping of the Thioacylglyceraldehyde-3-phosphate Dehydrogenase Intermediate from Bacillus stearothermophilus: DIRECT EVIDENCE FOR A FLIP-FLOP MECHANISM. J.Biol.Chem. (2008)

Release Date

2008-06-17

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

Glyceraldehyde-3-phosphate dehydrogenase

Related Entries With Identical Sequence