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

Crystal structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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 18 PLIP interactions: 18 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:N.154, A:P.183, A:L.190, A:E.283, A:T.285 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.9: 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 15 PLIP interactions: 15 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:P.183, B:L.190 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:Y.231, A:P.232 Water bridges: A:D.215, A:D.215, A:P.228, A:L.230, A:E.234 GOL.3: 6 residues within 4Å: Chain A: N.229, L.230, Y.231, P.232, P.233, S.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.229, A:S.243 Water bridges: A:S.243

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.210, A.214, D.216 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.210, A:A.214, A:D.216, H2O.1, H2O.1 CA.5: 2 residues within 4Å: Chain A: D.6, N.247 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.6, A:D.6, H2O.2, H2O.5, H2O.6 CA.10: 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.7, H2O.7, H2O.8

2 x T6J: 2-[(methylsulfonyl)methyl]-1H-benzimidazole(Non-covalent)

T6J.6: 9 residues within 4Å: Chain A: H.24, L.25, T.26, P.27, F.49 Chain B: V.28, L.29, T.30 Ligands: NA.17 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.29, A:P.27 Hydrogen bonds: B:T.30, B:T.30 T6J.13: 8 residues within 4Å: Chain A: V.28, L.29, T.30 Chain B: H.24, L.25, T.26, P.27, F.49 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.27, A:L.29 Water bridges: B:L.25 Hydrogen bonds: A:T.30

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

EDO.7: 5 residues within 4Å: Chain A: E.13, H.16, R.20, L.168, N.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.13, A:R.20 Water bridges: A:R.20, A:N.172 EDO.14: 5 residues within 4Å: Chain B: Y.218, I.259, F.260, T.261, H.297 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.218, B:Y.218, B:T.261, B:T.261 Water bridges: B:T.261 EDO.15: 4 residues within 4Å: Chain B: M.150, V.151, H.152 Ligands: CL.18 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.151, B:H.152 EDO.16: 5 residues within 4Å: Chain A: H.24 Chain B: T.30, S.31, S.32, N.35 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:S.32, B:N.35, B:N.35, B:N.35, B:L.42 Hydrogen bonds: A:H.24

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

NA.8: 5 residues within 4Å: Chain A: K.56, H.87, P.153, V.159, Q.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.153, A:Q.163 NA.12: 2 residues within 4Å: Chain B: D.6, N.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.6 Water bridges: B:N.247 NA.17: 4 residues within 4Å: Chain A: F.49 Chain B: L.29, T.30 Ligands: T6J.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.30, B:T.30

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 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.7, H2O.11, H2O.12

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.18: 4 residues within 4Å: Chain B: T.81, H.82, H.87 Ligands: EDO.15 Ligand excluded by PLIP

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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