SMTL ID : 7nbc.1 (1 other biounit)

Crystal structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: 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 16 PLIP interactions: 16 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 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.15: 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 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.55, B:K.56 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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.229, L.230, Y.231, P.232, S.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.243 Water bridges: A:S.243, A:S.243 GOL.3: 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.6: 5 residues within 4Å: Chain A: Y.218, I.259, F.260, T.261, H.297 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.261, A:T.261, A:T.261, A:H.297 Water bridges: A:Y.218, A:Y.218, A:T.261 GOL.9: 4 residues within 4Å: Chain A: E.13, H.16, L.168, N.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.16 GOL.10: 3 residues within 4Å: Chain A: D.6, N.247 Ligands: MG.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.6, A:N.247, A:N.247 GOL.16: 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 GOL.22: 5 residues within 4Å: Chain B: Y.218, K.221, L.222, D.258, I.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.218 Water bridges: B:D.258, B:D.258

3 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.2, H2O.3 CA.11: 2 residues within 4Å: Chain A: P.69 Ligands: EDO.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.69, H2O.1, H2O.3, H2O.4, H2O.4 CA.17: 3 residues within 4Å: Chain B: E.210, A.214, D.216 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.210, B:A.214, B:D.216, H2O.11, H2O.11

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.6, N.247 Ligands: GOL.10 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.6, H2O.2, H2O.8

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

EDO.7: 6 residues within 4Å: Chain A: N.213, N.229, L.230, Y.231, P.232, P.233 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.230, A:Y.231, A:P.232 Water bridges: A:E.234 EDO.8: 3 residues within 4Å: Chain A: P.69, D.70 Ligands: CA.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.70 EDO.20: 4 residues within 4Å: Chain B: L.67, V.68, I.149, M.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.150 Water bridges: B:V.68, B:V.68 EDO.21: 4 residues within 4Å: Chain B: F.43, V.174, P.175, L.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.176

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

NA.12: 3 residues within 4Å: Chain A: L.168, L.171, N.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.172 NA.13: 4 residues within 4Å: Chain A: L.67, E.156, P.157, A.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.158 NA.14: 3 residues within 4Å: Chain A: R.20, D.21, I.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.21

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.18: 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 BP4: biphenyl-4-ylacetic acid(Non-covalent)

BP4.19: 7 residues within 4Å: Chain B: T.81, H.82, S.83, H.87, V.151, H.152, P.153 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.81, B:H.82, B:S.83, B:V.151 Salt bridges: B:H.82, B:H.87 pi-Stacking: B:H.152

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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