SMTL ID : 6zuj.2 (1 other biounit)

Human serine racemase holoenzyme from 20% DMSO soak (XChem crystallographic fragment screen).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.20, D.21, S.22, I.23, K.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.20, A:K.51, A:K.51 EDO.9: 5 residues within 4Å: Chain B: F.43, V.174, P.175, L.176, N.307 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.176 Water bridges: B:N.307, B:N.307, B:N.307 EDO.10: 4 residues within 4Å: Chain B: N.18, R.65, S.66, L.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.18, B:R.65, B:L.67 EDO.11: 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.12: 3 residues within 4Å: Chain B: Q.36, L.37, G.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.37 EDO.13: 5 residues within 4Å: Chain A: H.24 Chain B: T.30, S.31, S.32, N.35 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.32, A:H.24 Water bridges: B:N.35, 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.1 CA.6: 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.5, H2O.5

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.4: 2 residues within 4Å: Chain A: T.30 Chain B: F.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.30, A:T.30 NA.5: 1 residues within 4Å: Chain B: D.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.178

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

PGE.7: 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:V.151 PGE.14: 5 residues within 4Å: Chain B: N.229, P.232, P.233, K.241, S.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.241, B:K.241, B:S.243

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

DMS.8: 5 residues within 4Å: Chain B: Y.218, I.259, F.260, T.261, H.297 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: 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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