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

Crystal structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 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.5: 5 residues within 4Å: Chain A: F.43, V.174, P.175, L.176, N.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.174, A:L.176, A:N.307 EDO.6: 4 residues within 4Å: Chain A: L.67, I.149, M.150, E.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.150, A:E.156 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 Water bridges: A:N.213, A:E.234 EDO.8: 4 residues within 4Å: Chain A: T.30, S.31, S.32, N.35 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.35, A:N.35, A:N.41 EDO.15: 6 residues within 4Å: Chain A: T.81, H.82, M.150, V.151, H.152, P.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.81, A:T.81, A:H.82 Water bridges: A:H.152 EDO.20: 4 residues within 4Å: Chain B: F.43, V.174, P.175, L.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.174, B:L.176 EDO.21: 4 residues within 4Å: Chain B: S.22, R.65, L.97, E.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.65, B:L.97, B:E.98 EDO.22: 4 residues within 4Å: Chain B: Q.36, L.37, T.38, G.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.37 Water bridges: B:G.39, B:Q.299 EDO.23: 4 residues within 4Å: Chain B: T.30, S.31, S.32, N.35 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.30, B:T.30 Water bridges: B:S.32, B:N.35, B:N.35

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

NA.2: 1 residues within 4Å: Chain A: D.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.178 NA.4: 2 residues within 4Å: Chain A: D.6, N.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.247 Water bridges: A:N.247 NA.11: 1 residues within 4Å: Chain A: P.69 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.69 NA.16: 4 residues within 4Å: Chain A: H.16, L.168, N.172 Chain B: E.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.13, A:H.16, A:N.172 NA.17: 2 residues within 4Å: Chain B: P.27, F.49 No protein-ligand interaction detected (PLIP) NA.18: 1 residues within 4Å: Chain B: D.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.178

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.2, H2O.2, H2O.4 CA.19: 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.13, H2O.13, H2O.13

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 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:S.243, A:S.243 Water bridges: A:S.243 GOL.10: 2 residues within 4Å: Chain A: L.29, T.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.30, A:T.30 GOL.12: 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.25: 6 residues within 4Å: Chain B: Y.218, D.258, I.259, F.260, T.261, H.297 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.258, B:T.261, B:T.261 Water bridges: B:Y.218, B:T.261, B:T.261

4 x W0D: N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide(Non-covalent)

W0D.13: 14 residues within 4Å: Chain A: S.84, G.85, N.86, G.88, Q.89, T.92, I.104, K.114, A.117, I.118, Y.121, D.238, N.316 Ligands: W0D.14 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.104, A:I.118, A:Y.121 Hydrogen bonds: A:S.84 Water bridges: A:G.85, A:Q.89, A:Q.89 W0D.14: 8 residues within 4Å: Chain A: D.238, P.284, N.316, V.317, D.318, S.322, W.325 Ligands: W0D.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.284, A:V.317, A:W.325 Hydrogen bonds: A:D.238, A:N.316, A:D.318 W0D.27: 14 residues within 4Å: Chain B: S.83, S.84, G.85, N.86, G.88, Q.89, T.92, I.104, K.114, I.118, Y.121, D.238, N.316 Ligands: W0D.28 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.104, B:Y.121 Hydrogen bonds: B:S.84, B:Q.89, B:K.114 W0D.28: 8 residues within 4Å: Chain B: I.236, D.238, P.284, N.316, V.317, D.318, S.321 Ligands: W0D.27 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.236, B:P.284, B:V.317, B:D.318 Hydrogen bonds: B:D.238, B:N.316, B:D.318 Water bridges: B:D.238

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

PGE.24: 6 residues within 4Å: Chain B: N.229, Y.231, 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 PGE.26: 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:M.150

1 x MG: MAGNESIUM ION(Non-covalent)

MG.29: 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.17, H2O.18

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
DDD

Serine racemase

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