SMTL ID : 2d2i.2 (1 other biounit)

Crystal Structure of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. complexed with Nadp+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: S.154, T.156, T.212, T.213, G.214, A.215 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.154, A:S.154, A:T.156, A:T.213, A:G.214, A:A.215 Water bridges: A:T.212 SO4.2: 5 residues within 4Å: Chain A: T.185, D.187, R.200, R.236 Ligands: NAP.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.185 Water bridges: A:R.236, A:R.236 Salt bridges: A:R.200, A:R.236 SO4.4: 6 residues within 4Å: Chain B: S.154, T.156, T.212, T.213, G.214, A.215 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.154, B:T.156, B:G.214, B:A.215 Water bridges: B:T.213 SO4.5: 5 residues within 4Å: Chain B: T.185, D.187, R.200, R.236 Ligands: NAP.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.185, B:T.185, B:D.187 Water bridges: B:R.200, B:R.200 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 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.154, C:T.156, C:T.213, C:G.214, C:A.215 Water bridges: C:S.154 SO4.8: 5 residues within 4Å: Chain C: T.185, D.187, R.200, R.236 Ligands: NAP.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.187 Salt bridges: C:R.200, C:R.236 SO4.10: 4 residues within 4Å: Chain D: S.154, T.213, G.214, A.215 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.154, D:T.213, D:G.214, D:A.215 Water bridges: D:S.154, D:G.214, D:R.236, D:R.236, D:R.236 SO4.11: 5 residues within 4Å: Chain D: T.185, D.187, R.200, R.236 Ligands: NAP.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.185, D:D.187 Water bridges: D:T.185, D:R.200, D:R.200 Salt bridges: D:R.200, D:R.236

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.3: 22 residues within 4Å: Chain A: G.9, F.10, 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 Chain D: S.194 Ligands: SO4.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.13, A:Y.322 Hydrogen bonds: A:F.10, A:R.12, A:I.13, A:T.37, A:T.37, A:R.80, A:R.80, A:T.122, A:N.318 Water bridges: A:N.8, A:G.11, A:G.14, A:R.15, A:G.100, A:T.122, D:S.194 NAP.6: 23 residues within 4Å: Chain B: G.9, F.10, G.11, R.12, I.13, N.35, T.37, D.79, 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 Chain C: S.194 Ligands: SO4.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.322 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:N.35, B:T.37, B:T.37, B:R.80, B:R.80, B:T.122, B:N.318 Water bridges: B:G.11, B:G.100, B:L.186, B:L.186, B:E.319 Salt bridges: B:R.80 NAP.9: 24 residues within 4Å: Chain B: S.194 Chain C: G.9, F.10, G.11, R.12, I.13, N.35, T.37, D.79, R.80, S.98, T.99, G.100, V.101, F.102, T.122, A.123, C.155, T.185, L.186, N.318, E.319, Y.322 Ligands: SO4.8 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.13, C:Y.322 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:N.35, C:T.37, C:R.80, C:R.80, C:N.318 Water bridges: C:F.10, C:G.11, C:G.14, C:T.37, C:L.186 Salt bridges: C:R.80 NAP.12: 24 residues within 4Å: Chain A: S.194 Chain D: G.9, F.10, G.11, R.12, I.13, N.35, T.37, D.79, R.80, S.98, T.99, G.100, V.101, F.102, T.122, A.123, C.155, T.185, L.186, N.318, E.319, Y.322 Ligands: SO4.11 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.13, D:Y.322, D:Y.322 Hydrogen bonds: D:R.12, D:I.13, D:N.35, D:R.80, D:R.80, D:N.318 Water bridges: D:G.11, D:T.37, D:T.37, D:G.100, D:T.122, D:L.186, D:L.186 Salt bridges: D:R.80 pi-Cation interactions: D:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitatani, T. et al., Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP. Acta Crystallogr.,Sect.F (2006)

Release Date

2006-07-11

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

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