SMTL ID : 3rvd.3 (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 Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-2-mer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: 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, T.184, N.317, Y.321 Chain C: E.76 Chain E: S.193 16 PLIP interactions: 13 interactions with chain A, 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: A:I.13, A:Y.321 Hydrogen bonds: A:F.10, A:R.12, A:I.13, A:T.37, A:R.81, A:R.81, A:N.317, E:S.193, E:S.193, C:E.76 Water bridges: A:G.11, A:G.14, A:G.185, A:G.185 NAD.4: 24 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, E.318, Y.321 Chain F: S.193 Ligands: SO4.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:I.13, B:Y.321 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:T.37, B:R.81, B:T.123, B:N.317, F:S.193 Water bridges: B:F.10, B:R.15 pi-Cation interactions: B:R.81 NAD.9: 23 residues within 4Å: Chain A: S.193 Chain C: E.73, Y.80 Chain E: 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, T.184, N.317, Y.321 16 PLIP interactions: 13 interactions with chain E, 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: E:I.13, E:Y.321 Hydrogen bonds: E:F.10, E:R.12, E:I.13, E:T.37, E:R.81, E:R.81, E:N.317, C:D.81, A:S.193, A:S.193 Water bridges: E:G.11, E:G.14, E:G.185, E:G.185 NAD.12: 25 residues within 4Å: Chain B: S.193 Chain D: E.73 Chain F: 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, E.318, Y.321 Ligands: SO4.13 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:I.13, F:Y.321 Hydrogen bonds: F:F.10, F:R.12, F:I.13, F:T.37, F:R.81, F:T.123, F:N.317, B:S.193 Water bridges: F:F.10, F:R.15 pi-Cation interactions: F:R.81

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

SO4.2: 5 residues within 4Å: Chain A: E.257, N.260, R.264, D.279, S.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.260, A:D.279 Salt bridges: A:R.264 SO4.3: 3 residues within 4Å: Chain A: R.198 Chain B: S.299, L.300 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.198 Hydrogen bonds: B:S.299, B:S.299 SO4.5: 5 residues within 4Å: Chain B: T.184, D.186, R.199, R.235 Ligands: NAD.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.235 Water bridges: B:R.199, B:R.199 Salt bridges: B:R.199 SO4.6: 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:G.213, B:A.214 Water bridges: B:T.155 SO4.7: 4 residues within 4Å: Chain B: I.130, P.131, T.132, L.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.130, B:T.132, B:L.220 SO4.8: 4 residues within 4Å: Chain B: R.288 Chain E: T.52, L.53, G.54 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Salt bridges: B:R.288 Water bridges: E:R.288 SO4.10: 5 residues within 4Å: Chain E: E.257, N.260, R.264, D.279, S.298 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.260, E:D.279 Salt bridges: E:R.264 SO4.11: 3 residues within 4Å: Chain E: R.198 Chain F: S.299, L.300 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Salt bridges: E:R.198 Hydrogen bonds: F:S.299, F:S.299 SO4.13: 5 residues within 4Å: Chain F: T.184, D.186, R.199, R.235 Ligands: NAD.12 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.235 Water bridges: F:R.199, F:R.199 Salt bridges: F:R.199 SO4.14: 5 residues within 4Å: Chain F: S.153, T.155, T.212, G.213, A.214 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.153, F:S.153, F:T.155, F:T.212, F:G.213, F:A.214 Water bridges: F:T.155 SO4.15: 4 residues within 4Å: Chain F: I.130, P.131, T.132, L.220 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:I.130, F:T.132, F:L.220 SO4.16: 4 residues within 4Å: Chain A: T.52, L.53, G.54 Chain F: R.288 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Salt bridges: F:R.288 Water bridges: A:R.288

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: ABEF
Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform): CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
Q

E
O

F
Q

C
K

D
L

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)

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