SMTL ID : 3b20.2 (1 other biounit)

Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with NADfrom Synechococcus elongatus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: S.154, T.156, T.213, G.214, A.215 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.154, A:T.156, A:T.156, A:T.213, A:G.214, A:A.215 Water bridges: A:T.156, A:T.157, A:G.214 SO4.2: 5 residues within 4Å: Chain A: T.185, D.187, R.200, R.236 Ligands: NAD.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.185, A:T.185 Salt bridges: A:R.200, A:R.236 SO4.4: 5 residues within 4Å: Chain B: S.154, T.156, T.213, G.214, A.215 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.154, B:G.214, B:A.215 Water bridges: B:T.157, B:T.157 SO4.5: 5 residues within 4Å: Chain B: T.185, D.187, R.200, R.236 Ligands: NAD.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.185, B:T.185 Water bridges: B:D.187, B:D.187 Salt bridges: B:R.200, B:R.236 SO4.7: 5 residues within 4Å: Chain C: S.154, T.156, T.213, G.214, A.215 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.154, C:T.156, C:T.213, C:G.214, C:A.215 SO4.8: 5 residues within 4Å: Chain C: T.185, D.187, R.200, R.236 Ligands: NAD.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.187, C:D.187 Salt bridges: C:R.200, C:R.236 SO4.10: 5 residues within 4Å: Chain D: S.154, T.156, T.213, G.214, A.215 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.154, D:S.154, D:T.213, D:T.213, D:G.214, D:A.215 SO4.11: 5 residues within 4Å: Chain D: T.185, D.187, R.200, R.236 Ligands: NAD.12 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.200, D:R.236

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

NAD.3: 22 residues within 4Å: Chain A: G.9, F.10, G.11, R.12, I.13, N.35, N.36, T.37, R.80, S.98, T.99, G.100, F.102, T.122, A.123, C.155, T.185, L.186, N.318, E.319, Y.322 Ligands: SO4.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.13, A:Y.322 Hydrogen bonds: A:F.10, A:F.10, A:R.12, A:I.13, A:N.36, A:R.80, A:R.80, A:T.122, A:N.318, A:E.319 Water bridges: A:N.8, A:G.11, A:G.14, A:G.100, A:T.122, A:L.186 NAD.6: 22 residues within 4Å: Chain B: G.9, F.10, G.11, R.12, I.13, N.35, N.36, T.37, D.79, R.80, S.98, T.99, G.100, T.122, A.123, C.155, T.185, L.186, N.318, E.319, Y.322 Ligands: SO4.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.322 Hydrogen bonds: B:F.10, B:F.10, B:G.11, B:R.12, B:I.13, B:N.35, B:T.37, B:R.80, B:T.122, B:N.318 Water bridges: B:N.8 NAD.9: 21 residues within 4Å: Chain B: S.194 Chain C: G.9, G.11, R.12, I.13, N.35, T.37, R.80, S.98, T.99, G.100, V.101, T.122, A.123, C.155, T.185, L.186, N.318, E.319, Y.322 Ligands: SO4.8 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.13, C:Y.322 Hydrogen bonds: C:R.12, C:I.13, C:N.35, C:T.37, C:R.80, C:R.80, C:N.318, B:S.194, B:S.194 Water bridges: C:R.80 NAD.12: 23 residues within 4Å: Chain A: S.194 Chain D: G.9, F.10, G.11, R.12, I.13, N.35, T.37, R.80, S.98, T.99, G.100, F.102, T.122, A.123, C.155, H.182, T.185, L.186, N.318, E.319, Y.322 Ligands: SO4.11 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:I.13 Hydrogen bonds: D:R.12, D:I.13, D:R.80, D:R.80, D:N.318, A:S.194, A:S.194 Water bridges: D:F.10, D:R.15, D:T.37, D:G.100, D:T.122 pi-Stacking: D:Y.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumura, H. et al., Structure Basis for the Regulation of Glyceraldehyde-3-Phosphate Dehydrogenase Activity via the Intrinsically Disordered Protein CP12. Structure (2011)

Release Date

2012-01-11

Peptides

Glyceraldehyde 3-phosphate dehydrogenase (NADP+): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

Glyceraldehyde 3-phosphate dehydrogenase (NADP+)

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