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

Crystal structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 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:N.154, A:G.185, A:G.186, A:G.187, A:G.188, A:M.189, A:S.313 Water bridges: A:P.153, A:P.183, A:L.190, A:E.283, A:T.285 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.8: 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: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

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

EDO.2: 5 residues within 4Å: Chain A: R.20, D.21, S.22, I.23, H.24 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.20, A:I.23, A:H.24, A:L.25, A:K.51 EDO.12: 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 EDO.13: 4 residues within 4Å: Chain B: S.22, R.65, L.97, E.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.65, B:L.97 EDO.14: 3 residues within 4Å: Chain B: L.37, T.38, G.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.37 Water bridges: B:G.39 EDO.15: 5 residues within 4Å: Chain A: H.24 Chain B: T.30, S.31, S.32, N.35 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.24, B:T.30, B:S.32 Water bridges: B:N.35, B:N.35, B:N.35

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.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

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

NA.4: 2 residues within 4Å: Chain A: D.6, N.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.6 NA.5: 3 residues within 4Å: Chain A: T.30 Chain B: P.27, F.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.30 NA.9: 1 residues within 4Å: Chain B: D.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.178

1 x U78: ~{N}-[2-(2-methylphenyl)ethyl]ethanamide(Non-covalent)

U78.6: 10 residues within 4Å: Chain A: S.84, G.85, G.88, Q.89, T.92, I.104, K.114, A.117, I.118, Y.121 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.89, A:I.104, A:I.118 Hydrogen bonds: A:S.84

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: E.13, L.168 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.13, H2O.3 MG.19: 2 residues within 4Å: Chain B: D.6, N.247 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.6, B:D.6, H2O.9, H2O.13

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

PG0.11: 7 residues within 4Å: Chain B: T.81, H.82, H.87, M.150, V.151, H.152, P.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.81, B:H.82 Water bridges: B:H.152

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

PGE.16: 5 residues within 4Å: Chain B: N.229, P.232, P.233, K.241, S.243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.241, B:K.241, B:S.243 Water bridges: B:S.243

1 x OXE: ORTHO-XYLENE(Non-covalent)

OXE.17: 9 residues within 4Å: Chain B: S.83, S.84, G.85, G.88, Q.89, T.92, I.104, I.118, Y.121 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.89, B:I.104, B:I.118, B:Y.121, B:Y.121

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 6 residues within 4Å: Chain B: Y.218, D.258, I.259, F.260, T.261, H.297 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.218, B:Y.218, B:D.258, B:T.261, B:T.261 Water bridges: B:T.261, B:T.261

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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