SMTL ID : 5tso.2 (1 other biounit)

CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PIG MUSCLE COMPLEXED WITH ORTHOPHENANTHROLINE AT 1.90 ANGSTROM RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

8 x PHN: 1,10-PHENANTHROLINE(Non-covalent)

PHN.1: 6 residues within 4Å: Chain A: M.131, H.135, P.267, K.269, I.271, D.324 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.271 PHN.2: 6 residues within 4Å: Chain A: V.2, K.25, V.327, A.330, S.331 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.330 Hydrogen bonds: A:V.2 PHN.10: 6 residues within 4Å: Chain B: M.131, H.135, P.267, K.269, I.271, D.324 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.271 PHN.11: 6 residues within 4Å: Chain B: V.2, K.25, V.327, A.330, S.331 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.330 Hydrogen bonds: B:V.2 PHN.19: 6 residues within 4Å: Chain C: M.131, H.135, P.267, K.269, I.271, D.324 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.271 PHN.20: 6 residues within 4Å: Chain C: V.2, K.25, V.327, A.330, S.331 Ligands: GOL.27 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.330 Hydrogen bonds: C:V.2 PHN.28: 6 residues within 4Å: Chain D: M.131, H.135, P.267, K.269, I.271, D.324 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.271 PHN.29: 6 residues within 4Å: Chain D: V.2, K.25, V.327, A.330, S.331 Ligands: GOL.36 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.330 Hydrogen bonds: D:V.2

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

SO4.3: 6 residues within 4Å: Chain A: P.122, S.149, T.152, T.209, G.210, A.211 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.149, A:T.152, A:T.209, A:T.209, A:G.210 Water bridges: A:S.149, A:C.150, A:T.151, A:T.151 SO4.4: 4 residues within 4Å: Chain A: T.180, T.182, R.232 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.180 Water bridges: A:A.181, A:A.181, A:R.232, A:R.232, A:R.232 Salt bridges: A:R.232 SO4.12: 6 residues within 4Å: Chain B: P.122, S.149, T.152, T.209, G.210, A.211 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.149, B:T.152, B:T.209, B:T.209, B:G.210 Water bridges: B:S.149, B:C.150, B:T.151, B:T.151 SO4.13: 4 residues within 4Å: Chain B: T.180, T.182, R.232 Ligands: NAD.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.180 Water bridges: B:A.181, B:A.181, B:R.232, B:R.232, B:R.232 Salt bridges: B:R.232 SO4.21: 6 residues within 4Å: Chain C: P.122, S.149, T.152, T.209, G.210, A.211 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.149, C:T.209, C:G.210 Water bridges: C:S.149, C:C.150, C:T.151, C:T.152 SO4.22: 4 residues within 4Å: Chain C: T.180, T.182, R.232 Ligands: NAD.23 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.180, C:T.180, C:T.182 Water bridges: C:A.181, C:A.181, C:R.232, C:R.232, C:R.232 Salt bridges: C:R.232 SO4.30: 6 residues within 4Å: Chain D: P.122, S.149, T.152, T.209, G.210, A.211 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.149, D:T.209, D:G.210 Water bridges: D:S.149, D:C.150, D:T.151, D:T.152 SO4.31: 4 residues within 4Å: Chain D: T.180, T.182, R.232 Ligands: NAD.32 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.180, D:T.180, D:T.182 Water bridges: D:A.181, D:A.181, D:R.232, D:R.232, D:R.232 Salt bridges: D:R.232

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

NAD.5: 25 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, C.150, A.181, N.314, Y.318 Chain C: P.189 Ligands: SO4.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.12, A:I.12, A:Y.318 Hydrogen bonds: A:N.7, A:F.9, A:F.9, A:R.11, A:I.12, A:N.32, A:R.78, A:N.314 Water bridges: A:G.10, A:G.13, A:G.98, A:S.120, A:A.181, A:A.181 pi-Stacking: A:F.35 NAD.14: 25 residues within 4Å: Chain B: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, C.150, A.181, N.314, Y.318 Chain D: P.189 Ligands: SO4.13 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.12, B:I.12, B:Y.318 Hydrogen bonds: B:N.7, B:F.9, B:F.9, B:R.11, B:I.12, B:N.32, B:R.78, B:N.314 Water bridges: B:G.10, B:G.13, B:G.98, B:S.120, B:A.181, B:A.181 pi-Stacking: B:F.35 NAD.23: 25 residues within 4Å: Chain A: P.189 Chain C: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, C.150, A.181, N.314, Y.318 Ligands: SO4.22 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.12, C:I.12, C:Y.318 Hydrogen bonds: C:N.7, C:F.9, C:F.9, C:R.11, C:I.12, C:N.32, C:R.78, C:N.314 Water bridges: C:G.10, C:G.13, C:G.98, C:S.120, C:A.181, C:A.181 pi-Stacking: C:F.35 NAD.32: 25 residues within 4Å: Chain B: P.189 Chain D: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, C.150, A.181, N.314, Y.318 Ligands: SO4.31 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.12, D:I.12, D:Y.318 Hydrogen bonds: D:N.7, D:F.9, D:F.9, D:R.11, D:I.12, D:N.32, D:R.78, D:N.314 Water bridges: D:G.10, D:G.13, D:G.98, D:S.120, D:A.181, D:A.181 pi-Stacking: D:F.35

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: N.302, D.303, H.304 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: Y.274, T.275, V.279, D.283, F.284, T.292 Chain B: Y.47, K.53 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: S.264, K.269, G.270, H.289 Ligand excluded by PLIP GOL.9: 2 residues within 4Å: Chain A: K.25 Ligands: PHN.2 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain B: N.302, D.303, H.304 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: Y.47, K.53 Chain B: Y.274, T.275, V.279, D.283, F.284, T.292 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: S.264, K.269, G.270, H.289 Ligand excluded by PLIP GOL.18: 2 residues within 4Å: Chain B: K.25 Ligands: PHN.11 Ligand excluded by PLIP GOL.24: 3 residues within 4Å: Chain C: N.302, D.303, H.304 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain C: Y.274, T.275, V.279, D.283, F.284, T.292 Chain D: Y.47, K.53 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain C: S.264, K.269, G.270, H.289 Ligand excluded by PLIP GOL.27: 2 residues within 4Å: Chain C: K.25 Ligands: PHN.20 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain D: N.302, D.303, H.304 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain C: Y.47, K.53 Chain D: Y.274, T.275, V.279, D.283, F.284, T.292 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain D: S.264, K.269, G.270, H.289 Ligand excluded by PLIP GOL.36: 2 residues within 4Å: Chain D: K.25 Ligands: PHN.29 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dimova, M. et al., Novel Enhancer Binding Site Found In Bacteria And Eukaryota But Not In Archea. To Be Published

Release Date

2017-05-03

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
S

C
S

D
S

Glyceraldehyde-3-phosphate dehydrogenase

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