SMTL ID : 7nbh.2 (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

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

EDO.1: 6 residues within 4Å: Chain A: R.20, D.21, S.22, I.23, H.24, K.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.20 Water bridges: A:H.24, A:K.51 EDO.6: 6 residues within 4Å: Chain A: T.81, H.82, M.150, V.151, H.152, P.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.81, A:H.82 EDO.9: 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.10: 4 residues within 4Å: Chain B: L.67, V.68, I.149, M.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.150 EDO.11: 4 residues within 4Å: Chain B: N.229, P.232, P.233, S.243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.229, B:S.243 Water bridges: B:K.241, B:S.243 EDO.13: 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, B:S.32 Water bridges: B:N.35, B:N.35

2 x CA: CALCIUM ION(Non-covalent)

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

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

NA.3: 2 residues within 4Å: Chain A: D.6, N.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.6 NA.15: 1 residues within 4Å: Chain B: H.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.82, B:R.135 NA.16: 1 residues within 4Å: Chain B: P.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.11

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

W0D.4: 13 residues within 4Å: Chain A: 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.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.89, A:I.104, A:I.118, A:Y.121 Hydrogen bonds: A:S.84, A:Q.89, A:K.114 W0D.5: 6 residues within 4Å: Chain A: D.238, P.284, N.316, V.317, D.318 Ligands: W0D.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.284, A:V.317 Hydrogen bonds: A:D.238, A:N.316, A:D.318 Water bridges: A:D.238

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain B: L.29, T.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.30, B:T.30 GOL.12: 6 residues within 4Å: Chain B: R.20, D.21, S.22, I.23, H.24, K.51 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.14: 5 residues within 4Å: Chain B: Y.218, K.221, L.222, D.258, I.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.218, B:D.258, B:I.259

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 4 residues within 4Å: Chain A: E.13, L.168 Chain B: F.9, E.13 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.13, A:E.13, H2O.2

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

CL.18: 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
BBB

B
CCC

Serine racemase

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