SMTL ID : 6zuj.1 (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

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

PGE.1: 4 residues within 4Å: Chain A: H.152, Q.155, E.156, N.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.247 Water bridges: A:H.152, A:H.152, A:N.247 PGE.14: 3 residues within 4Å: Chain A: F.49 Chain B: L.29, T.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.30 PGE.22: 3 residues within 4Å: Chain B: R.20, D.21, L.25 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.25, B:L.25

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

DMS.2: 5 residues within 4Å: Chain A: Y.218, I.259, F.260, T.261, H.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.261

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.178 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.178, H2O.3, H2O.3, H2O.9, H2O.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.15: 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.12, H2O.13

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

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 No protein-ligand interaction detected (PLIP) NA.12: 2 residues within 4Å: Chain A: E.13, L.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.13 Water bridges: A:N.172

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

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 Water bridges: A:N.307, 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: 5 residues within 4Å: Chain A: 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: 5 residues within 4Å: Chain A: T.30, S.32, N.35 Chain B: H.24 Ligands: GOL.19 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.32, A:N.35, A:N.35, A:N.41 EDO.16: 3 residues within 4Å: Chain B: D.6, L.246, N.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.246 Water bridges: B:D.6, B:D.6 EDO.17: 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.18: 3 residues within 4Å: Chain B: N.229, P.232, P.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.229, B:S.243 EDO.20: 5 residues within 4Å: Chain A: H.24 Chain B: T.30, S.31, S.32, N.35 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.30, B:S.32 Water bridges: B:T.30, B:T.30, B:N.35, B:L.42, A:H.24

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: N.229, L.230, Y.231, P.232, P.233, K.241, S.243 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.241, A:S.243, A:S.243 Water bridges: A:N.229, A:S.243 GOL.13: 5 residues within 4Å: Chain A: L.29, T.30 Chain B: H.24, P.27, F.49 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:F.49, A:T.30, A:T.30 Hydrogen bonds: A:T.30 GOL.19: 6 residues within 4Å: Chain B: D.21, S.22, I.23, H.24, K.51 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.22, B:H.24 Water bridges: B:L.25 GOL.21: 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

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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