SMTL ID : 7nbd.1 (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 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.55, A:K.56, A:V.240 Hydrogen bonds: A:K.56, 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:N.154, A:L.190, A:E.283 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.10: 16 residues within 4Å: Chain B: F.55, K.56, N.86, N.154, 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:K.56, 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:P.153, B:P.153, B:L.190 Salt bridges: B:K.56 pi-Stacking: B:F.55

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: N.229, L.230, Y.231, P.232, P.233, S.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.243 Water bridges: A:S.243, A:S.243, A:S.243 GOL.3: 5 residues within 4Å: Chain A: Y.218, I.259, F.260, T.261, H.297 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.218, A:T.261, A:H.297 Water bridges: A:T.261, A:T.261, A:T.261 GOL.4: 5 residues within 4Å: Chain A: V.68, T.143, I.149, M.150, E.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.150 Water bridges: A:G.148 GOL.8: 5 residues within 4Å: Chain A: D.11, S.66, P.157, A.158, A.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.66, A:S.66 Water bridges: A:D.11, A:N.62 GOL.9: 4 residues within 4Å: Chain A: E.13, H.16, L.168, N.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.13, A:H.16 Water bridges: A:H.16 GOL.12: 3 residues within 4Å: Chain B: K.14, I.17, N.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.14, B:N.18, B:N.18

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.2, H2O.2, H2O.2 CA.13: 3 residues within 4Å: Chain B: E.210, A.214, D.216 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.210, B:A.214, H2O.14, H2O.17, H2O.18 CA.14: 1 residues within 4Å: Chain B: D.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.6, B:D.6, H2O.14, H2O.17

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: D.6, N.247 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.6, H2O.4, H2O.4, H2O.10, H2O.10

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

JFS.7: 10 residues within 4Å: Chain A: W.275, L.281, V.317, D.318, L.319, S.322 Chain B: W.275, L.281, V.317, L.319 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.281, A:L.281, A:L.319, B:W.275, B:W.275, B:L.281, B:L.281 pi-Stacking: A:W.275, B:W.275 Hydrogen bonds: B:V.317

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 4 residues within 4Å: Chain A: F.49 Chain B: L.29, T.30, M.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.30, B:M.278

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

EDO.15: 8 residues within 4Å: Chain B: V.80, T.81, H.82, S.83, H.87, L.91, M.150, V.151 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.82, B:S.83, B:V.151

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
AAA

B
CCC

Serine racemase

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