SMTL ID : 7nbg.1 (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: 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 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 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

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

EDO.2: 4 residues within 4Å: Chain A: H.152, Q.155, E.156, N.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.247 Water bridges: A:H.152, A:N.247 EDO.6: 5 residues within 4Å: Chain A: F.43, V.174, P.175, L.176, N.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.174, A:L.176, A:N.307 Water bridges: A:N.307 EDO.7: 4 residues within 4Å: Chain A: L.67, I.149, M.150, E.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.150, A:E.156 Water bridges: A:G.148 EDO.8: 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.9: 6 residues within 4Å: Chain A: T.30, S.31, S.32, N.35 Chain B: H.24 Ligands: GOL.21 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.35, A:N.35 EDO.18: 4 residues within 4Å: Chain B: D.6, L.246, N.247, P.250 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.6, B:L.246 EDO.19: 3 residues within 4Å: Chain B: L.67, I.149, M.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.150 Water bridges: B:M.150, B:E.156 EDO.20: 3 residues within 4Å: Chain B: N.229, P.232, S.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.229, B:S.243 EDO.22: 5 residues within 4Å: Chain A: H.24 Chain B: T.30, S.31, S.32, N.35 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.24, B:T.30, B:S.32 Water bridges: A:K.51, B:N.35, B:N.35

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

NA.3: 1 residues within 4Å: Chain A: D.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.178 NA.5: 2 residues within 4Å: Chain A: D.6, N.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.247 NA.11: 1 residues within 4Å: Chain A: P.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.69 NA.14: 3 residues within 4Å: Chain A: H.16, L.168, N.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.16, A:N.172 Water bridges: A:H.16 NA.24: 1 residues within 4Å: Chain B: H.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.82 Water bridges: B:R.135 NA.25: 1 residues within 4Å: Chain B: P.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.11

2 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.1, H2O.3 CA.17: 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.13, H2O.14

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 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 Water bridges: A:S.243, A:S.243, A:S.243 GOL.13: 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.16: 5 residues within 4Å: Chain A: L.29, T.30 Chain B: H.24, P.27, F.49 No protein-ligand interaction detected (PLIP) GOL.21: 7 residues within 4Å: Chain B: R.20, D.21, S.22, I.23, H.24, K.51 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.22, B:H.24 Water bridges: B:L.25, B:K.51 GOL.23: 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:D.258

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

U78.12: 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.89, A:I.104, A:I.118, A:I.118, A:Y.121, A:Y.121 Hydrogen bonds: A:S.84

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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