SMTL ID : 8pir.1

Crystal structure of Ser33 in complex with 3-PGA (3-phosphoglycerate)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: I.135, F.157, N.159, V.163, G.209, Y.210, G.211, H.212, I.213, Y.231, D.232, I.233, H.261, V.262, P.263, T.268, M.271, A.289, S.290, R.291, D.315, H.351, G.353, G.354 Chain B: R.45 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.135, A:N.159, A:V.163, A:I.213 Hydrogen bonds: A:Y.210, A:Y.210, A:H.212, A:I.213, A:I.233, A:V.262, A:R.291, A:D.315, A:G.354, B:R.45, B:R.45 Water bridges: A:G.211, A:G.214 Salt bridges: A:H.212 NAD.4: 25 residues within 4Å: Chain A: R.45 Chain B: I.135, F.157, V.163, G.209, Y.210, G.211, H.212, I.213, Y.231, D.232, I.233, I.236, H.261, V.262, P.263, T.268, M.271, A.289, S.290, R.291, D.315, H.351, G.353, G.354 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.135, B:V.163, B:I.213 Hydrogen bonds: B:Y.210, B:Y.210, B:H.212, B:I.213, B:I.233, B:V.262, B:R.291, B:D.315, B:G.353, B:G.354, A:R.45, A:R.45 Salt bridges: B:H.212 NAD.7: 26 residues within 4Å: Chain C: I.135, F.157, N.159, V.163, G.209, Y.210, G.211, H.212, I.213, Y.231, D.232, I.233, H.261, V.262, P.263, E.267, T.268, M.271, A.289, S.290, R.291, D.315, H.351, G.353, G.354 Chain D: R.45 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.135, C:N.159, C:V.163, C:I.213 Hydrogen bonds: C:Y.210, C:Y.210, C:H.212, C:I.213, C:I.233, C:V.262, C:R.291, C:D.315, C:D.315, C:G.353, C:G.354, D:R.45, D:R.45 Salt bridges: C:H.212 NAD.10: 25 residues within 4Å: Chain C: R.45 Chain D: I.135, F.157, V.163, G.209, Y.210, G.211, H.212, I.213, Y.231, D.232, I.233, I.236, H.261, V.262, P.263, T.268, M.271, A.289, S.290, R.291, D.315, H.351, G.353, G.354 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.135, D:V.163, D:I.213 Hydrogen bonds: D:Y.210, D:Y.210, D:H.212, D:H.212, D:I.213, D:I.233, D:V.262, D:R.291, D:D.315, D:G.353, D:G.354, C:R.45

4 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.2: 6 residues within 4Å: Chain A: R.111, S.112, C.134, I.135, G.136 Chain C: K.192 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.112, A:S.112, A:I.135, A:G.136 Salt bridges: A:R.111, C:K.192 3PG.5: 6 residues within 4Å: Chain B: R.111, S.112, C.134, I.135, G.136 Chain D: K.192 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.112, B:I.135, B:G.136 Salt bridges: B:R.111, D:K.192 3PG.8: 7 residues within 4Å: Chain A: K.192 Chain C: R.111, S.112, C.134, I.135, G.136, N.159 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Salt bridges: A:K.192, C:R.111 Hydrogen bonds: C:S.112, C:S.112, C:I.135, C:G.136, C:N.159 3PG.11: 6 residues within 4Å: Chain B: K.192 Chain D: R.111, S.112, C.134, I.135, G.136 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.112, D:I.135, D:G.136 Salt bridges: D:R.111, B:K.192

4 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.3: 11 residues within 4Å: Chain A: H.408, N.410, V.411, P.412, G.413, V.414, L.415, S.432, A.439 Chain B: N.426, I.427 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.413, A:V.414, A:L.415, A:S.432, A:S.432 Hydrophobic interactions: B:I.427 Water bridges: B:I.427 BU1.6: 11 residues within 4Å: Chain A: N.426, I.427 Chain B: H.408, N.410, V.411, P.412, G.413, V.414, L.415, S.432, A.439 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.413, B:V.414, B:L.415, B:S.432, B:S.432 Water bridges: B:K.416 BU1.9: 10 residues within 4Å: Chain C: H.408, N.410, V.411, P.412, G.413, V.414, L.415, S.432 Chain D: N.426, I.427 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.413, C:V.414, C:L.415, C:S.432, C:S.432 Hydrophobic interactions: D:I.427 BU1.12: 9 residues within 4Å: Chain C: N.426, I.427 Chain D: H.408, N.410, V.411, P.412, G.413, V.414, L.415 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.413, D:V.414, D:L.415, D:S.432, D:S.432 Hydrophobic interactions: C:I.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perrone, S. et al., Crystal structure of Ser33 in complex with 3-PGA (3-phosphoglycerate). To Be Published

Release Date

2025-01-15

Peptides

phosphoglycerate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
B

D
C

phosphoglycerate dehydrogenase

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