SMTL ID : 7nbf.1 (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: 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:N.154, A:G.185, A:G.186, A:G.187, A:G.188, A:M.189, A:S.313 Water bridges: A:K.56, A:P.153, A:L.190 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.12: 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

7 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.218, A:T.261, A:T.261, A:H.297 GOL.4: 4 residues within 4Å: Chain A: V.68, 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: 4 residues within 4Å: Chain A: E.13, H.16, L.168, N.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.16 Water bridges: A:H.16, A:H.16, A:R.20 GOL.13: 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.16: 5 residues within 4Å: Chain B: Y.218, K.221, L.222, D.258, I.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.218, B:I.259 GOL.19: 6 residues within 4Å: Chain B: R.20, D.21, S.22, I.23, H.24, K.51 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.21, B:H.24, B:K.51 Water bridges: B:L.25, B:K.51

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.1, H2O.2, H2O.2 CA.10: 1 residues within 4Å: Chain A: P.69 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:P.69, H2O.4, H2O.5, H2O.8 CA.14: 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.13, H2O.16, H2O.16

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.6, H2O.6, H2O.8, H2O.9

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 6 residues within 4Å: Chain A: N.213, N.229, L.230, Y.231, P.232, P.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.230, A:Y.231

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

T6J.9: 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: PGE.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.27, B:L.29 Water bridges: A:L.25 Hydrogen bonds: B:T.30 T6J.15: 9 residues within 4Å: Chain A: V.28, L.29, T.30 Chain B: H.24, L.25, T.26, P.27, F.49 Ligands: NA.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.29, B:P.27 Hydrogen bonds: A:T.30 Water bridges: B:H.24

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

NA.11: 4 residues within 4Å: Chain A: L.29, T.30 Chain B: F.49 Ligands: T6J.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.30, A:T.30

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

EDO.17: 4 residues within 4Å: Chain B: F.43, V.174, P.175, L.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.176 Water bridges: B:N.307, B:N.307

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

PGE.18: 5 residues within 4Å: Chain A: F.49 Chain B: L.29, T.30, M.278 Ligands: T6J.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.30, B:M.278

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

CL.20: 4 residues within 4Å: Chain B: T.81, H.82, H.87, V.151 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
AAA

B
CCC

Serine racemase

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