SMTL ID : 3rvd.2 (2 other biounits)

Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-2-mer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: N.8, G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, N.80, R.81, G.99, T.100, G.101, V.102, F.103, T.123, A.124, C.154, H.181, T.184, N.317, Y.321 Chain D: S.193 Chain F: E.76 Ligands: SO4.2 12 PLIP interactions: 1 interactions with chain F, 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: F:E.76, A:F.10, A:R.12, A:I.13, A:D.36, A:T.37, A:R.81, A:T.184, A:N.317, D:S.193 Hydrophobic interactions: A:I.13, A:Y.321 NAD.5: 23 residues within 4Å: Chain B: G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, N.80, R.81, G.99, T.100, G.101, V.102, F.103, T.123, A.124, C.154, T.184, N.317 Chain C: S.193 Chain E: E.76 Ligands: SO4.6 11 PLIP interactions: 9 interactions with chain B, 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: B:I.13 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:T.37, B:R.81, B:R.81, B:T.123, B:N.317, E:E.76, C:S.193 NAD.8: 25 residues within 4Å: Chain B: S.193 Chain C: N.8, G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, R.81, G.99, T.100, G.101, V.102, F.103, T.123, A.124, C.154, N.317, E.318, Y.321 Chain E: E.73, Y.80, D.81 14 PLIP interactions: 11 interactions with chain C, 1 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: C:I.13, C:Y.321 Hydrogen bonds: C:R.12, C:I.13, C:N.35, C:T.37, C:R.81, C:T.123, C:N.317, E:D.81, B:S.193, B:S.193 Water bridges: C:G.11, C:G.14 NAD.10: 23 residues within 4Å: Chain A: S.193 Chain D: G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, N.80, R.81, G.99, T.100, G.101, T.123, A.124, C.154, T.184, N.317, E.318, Y.321 Chain F: E.73, Y.80 18 PLIP interactions: 13 interactions with chain D, 2 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: D:I.13 Hydrogen bonds: D:G.9, D:F.10, D:R.12, D:I.13, D:N.35, D:T.37, D:R.81, D:T.123, D:N.317, A:S.193, A:S.193, F:E.73, F:Y.80, F:Y.80 Water bridges: D:G.11, D:G.14 pi-Stacking: D:Y.321

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

SO4.2: 5 residues within 4Å: Chain A: T.184, D.186, R.199, R.235 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.184, A:D.186, A:D.186, A:D.186 Salt bridges: A:R.199, A:R.235 SO4.3: 6 residues within 4Å: Chain A: S.153, T.155, S.211, T.212, G.213, A.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.153, A:G.213, A:A.214 SO4.4: 4 residues within 4Å: Chain A: E.257, N.260, R.264, S.298 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.264 SO4.6: 5 residues within 4Å: Chain B: T.184, D.186, R.199, R.235 Ligands: NAD.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.184, B:T.184 Salt bridges: B:R.199, B:R.235 SO4.7: 5 residues within 4Å: Chain B: S.153, T.155, T.212, G.213, A.214 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.153, B:S.153, B:T.155, B:T.212, B:T.212, B:G.213, B:A.214 SO4.9: 4 residues within 4Å: Chain C: E.257, N.260, R.264, S.298 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.257, C:E.257, C:S.298 Salt bridges: C:R.264 SO4.11: 4 residues within 4Å: Chain D: E.257, N.260, R.264, S.298 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.260 Salt bridges: D:R.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fermani, S. et al., Conformational Selection and Folding-upon-binding of Intrinsically Disordered Protein CP12 Regulate Photosynthetic Enzymes Assembly. J.Biol.Chem. (2012)

Release Date

2012-04-25

Peptides

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic: ABCD
Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform): EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
M

F
N

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)

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