SMTL ID : 3b1j.1

Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the presence of copper from Synechococcus elongatus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-4-4-mer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: 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, V.101, F.102, T.122, A.123, C.155, L.186, N.318, E.319, Y.322 Chain C: D.16, Y.23, D.24 Chain H: E.19 27 PLIP interactions: 22 interactions with chain A, 3 interactions with chain C, 1 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: A:I.13, A:Y.322 Hydrogen bonds: A:F.10, A:F.10, A:R.12, A:I.13, A:N.35, A:N.36, A:T.37, A:R.80, A:T.122, A:N.318, C:Y.23, C:D.24, H:E.19 Water bridges: A:N.8, A:N.8, A:G.11, A:G.14, A:R.15, A:T.37, A:T.37, A:R.80, A:G.100, A:G.100, C:I.22, F:S.194 NAD.3: 26 residues within 4Å: Chain B: N.8, 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, F.102, T.122, A.123, C.155, L.186, N.318, E.319, Y.322 Chain D: D.16, Y.23, D.24 Chain G: E.19 29 PLIP interactions: 23 interactions with chain B, 3 interactions with chain D, 2 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: B:I.13, B:Y.322 Hydrogen bonds: B:F.10, B:F.10, B:R.12, B:I.13, B:N.35, B:N.36, B:T.37, B:R.80, B:R.80, B:T.122, B:N.318, D:D.16, D:D.24, G:E.19, G:E.19 Water bridges: B:N.8, B:G.11, B:G.14, B:R.15, B:R.15, B:T.37, B:T.37, B:G.100, B:T.122, B:L.186, D:Y.23, E:S.194 NAD.5: 26 residues within 4Å: Chain D: E.19 Chain E: 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, V.101, F.102, T.122, A.123, C.155, L.186, N.318, E.319, Y.322 Chain G: D.16, Y.23, D.24 26 PLIP interactions: 18 interactions with chain E, 4 interactions with chain G, 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: E:I.13, E:Y.322 Hydrogen bonds: E:F.10, E:F.10, E:R.12, E:I.13, E:N.35, E:N.36, E:T.37, E:R.80, E:N.318, G:D.24, D:E.19, D:E.19 Water bridges: E:N.8, E:N.8, E:G.11, E:G.14, E:R.15, E:G.100, E:G.100, G:D.16, G:I.22, G:Y.23, B:S.194, B:S.194 NAD.7: 26 residues within 4Å: Chain C: E.19 Chain F: N.8, 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, F.102, T.122, A.123, C.155, L.186, N.318, E.319, Y.322 Chain H: D.16, Y.23, D.24 24 PLIP interactions: 20 interactions with chain F, 2 interactions with chain H, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: F:I.13, F:Y.322 Hydrogen bonds: F:F.10, F:F.10, F:R.12, F:I.13, F:N.35, F:N.36, F:T.37, F:R.80, F:R.80, F:N.318, H:Y.23, H:D.24, C:E.19 Water bridges: F:N.8, F:G.11, F:G.14, F:R.15, F:R.15, F:G.100, F:T.122, F:L.186, A:S.194

4 x CU: COPPER (II) ION(Non-covalent)

CU.2: 5 residues within 4Å: Chain A: S.154, C.155, T.156, H.182 Chain C: D.25 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Metal complexes: C:D.25, A:C.155, A:T.156 CU.4: 5 residues within 4Å: Chain B: C.155, T.156, H.182, Y.316 Chain D: D.25 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.155, B:T.156 CU.6: 5 residues within 4Å: Chain E: S.154, C.155, T.156, H.182 Chain G: D.25 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E Metal complexes: G:D.25, E:C.155, E:T.156 CU.8: 5 residues within 4Å: Chain F: C.155, T.156, H.182, Y.316 Chain H: D.25 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.155, F:T.156

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+): ABEF
CP12: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

D
D

G
C

H
D

Glyceraldehyde 3-phosphate dehydrogenase (NADP+)

CP12

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