SMTL ID : 8pis.2 (1 other biounit)

Crystal structure of Ser33 in complex with L-Serine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-4-4-mer

Ligands

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

NAD.1: 26 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, 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 Chain B: R.45 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.135, A:N.159, A:V.163 Hydrogen bonds: A:H.212, A:I.213, A:I.233, A:V.262, A:T.268, A:R.291, A:D.315, A:D.315, A:G.353, A:G.354, B:R.45, B:R.45 Salt bridges: A:H.212 NAD.4: 24 residues within 4Å: Chain A: R.45 Chain B: I.135, F.157, N.159, V.163, G.209, Y.210, G.211, H.212, I.213, D.232, I.233, H.261, V.262, P.263, T.268, A.289, S.290, R.291, D.315, V.316, H.351, G.353, G.354 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.135, B:N.159, B:V.163 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:D.315, B:G.353, B:G.354, A:R.45, A:R.45 Salt bridges: B:H.212 NAD.5: 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, V.234, I.236, H.261, V.262, P.263, T.268, A.289, S.290, R.291, D.315, H.351, G.353, G.354 Chain D: R.45 18 PLIP interactions: 17 interactions with chain C, 1 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:G.353, C:G.354, D:R.45 Water bridges: C:G.211, C:G.214 Salt bridges: C:H.212 NAD.7: 25 residues within 4Å: Chain C: R.45 Chain D: I.135, F.157, N.159, 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, A.289, S.290, R.291, D.315, H.351, G.353, G.354 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.135, D:N.159, D:V.163, D:I.213 Hydrogen bonds: D:Y.210, D:Y.210, 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, C:R.45 Salt bridges: D:H.212

4 x SER: SERINE(Non-covalent)

SER.2: 11 residues within 4Å: Chain A: H.408, N.410, V.411, P.412, G.413, L.415, S.432, A.439 Chain B: H.425, N.426, I.427 8 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: A:N.410, A:N.410, A:G.413, A:S.432, S.2, B:I.427 Water bridges: A:L.415 Salt bridges: A:H.408 SER.3: 9 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 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.410, B:G.413, B:V.414, B:L.415, A:I.427 Salt bridges: B:H.408 SER.6: 12 residues within 4Å: Chain C: H.408, R.409, N.410, V.411, P.412, G.413, V.414, L.415, S.432, A.439 Chain D: N.426, I.427 9 PLIP interactions: 1 Ligand-Ligand interactions, 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: S.6, C:R.409, C:N.410, C:V.411, C:G.413, C:V.414, C:S.432, D:I.427 Salt bridges: C:H.408 SER.8: 11 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, S.432, A.439 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.410, D:N.410, D:G.413, D:V.414, D:S.432, C:I.427 Water bridges: D:G.413, D:L.415 Salt bridges: D:H.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perrone, S. et al., Crystal structure of Ser33 in complex with L-Serine. To Be Published

Release Date

2025-01-15

Peptides

phosphoglycerate dehydrogenase: ABCD
phosphoglycerate dehydrogenase: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
I

F
N

G
Q

H
L

phosphoglycerate dehydrogenase

phosphoglycerate dehydrogenase

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