SMTL ID : 7nbd.2 (1 other biounit)

Crystal structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: F.55, K.56, N.86, V.184, G.185, G.186, G.187, G.188, M.189, G.239, V.240, E.283, T.285, S.313, G.314 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.55, A:K.56, A:V.240 Hydrogen bonds: A:N.86, A:G.185, A:G.186, A:G.187, A:G.188, A:M.189, A:S.313 Water bridges: A:N.154, A:P.183, A:L.190, A:T.285 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.8: 15 residues within 4Å: Chain B: F.55, K.56, N.86, V.184, G.185, G.186, G.187, G.188, M.189, G.239, V.240, E.283, T.285, S.313, G.314 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.55, B:K.56, B:V.240 Hydrogen bonds: B:N.86, B:N.154, B:G.185, B:G.186, B:G.187, B:G.188, B:M.189, B:S.313 Water bridges: B:N.86, B:P.183, B:L.190, B:E.283 Salt bridges: B:K.56 pi-Stacking: B:F.55

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: N.213, N.229, L.230, Y.231, P.232, P.233 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.229, A:L.230, A:Y.231, A:P.232 Water bridges: A:D.215, A:D.215, A:P.228, A:E.234 GOL.3: 6 residues within 4Å: Chain A: N.229, L.230, Y.231, P.232, P.233, S.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.229, A:S.243

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.210, A.214, D.216 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.210, A:A.214, A:D.216, H2O.1, H2O.1, H2O.2 CA.5: 2 residues within 4Å: Chain A: D.6, N.247 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.6, A:D.6, H2O.3, H2O.7 CA.9: 3 residues within 4Å: Chain B: E.210, A.214, D.216 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.210, B:A.214, B:D.216, H2O.9, H2O.9, H2O.9 CA.11: 4 residues within 4Å: Chain B: T.81, H.82, S.83, H.87 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.81, H2O.8, H2O.17

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: D.6, D.11, P.157, A.158, A.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.6 Water bridges: A:D.11, A:N.62 EDO.13: 1 residues within 4Å: Chain B: Q.296 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.296

1 x JFS: [4-(1H-benzimidazol-1-yl)phenyl]methanol(Non-covalent)

JFS.7: 8 residues within 4Å: Chain A: W.275, V.317, L.319 Chain B: W.275, L.281, V.317, L.319, S.322 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.275, A:W.275, B:W.275, B:L.281, B:V.317, B:L.319 Hydrogen bonds: A:V.317 pi-Stacking: A:W.275, B:W.275

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 1 residues within 4Å: Chain B: D.178 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.178, H2O.8, H2O.10, H2O.12

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 2 residues within 4Å: Chain B: D.6, N.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.247 Water bridges: B:D.6, B:N.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koulouris, C.R. et al., Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase. Commun Biol (2022)

Release Date

2021-03-03

Peptides

Serine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

B
DDD

Serine racemase

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