SMTL ID : 6zsp.1

Human serine racemase bound to ATP and malonate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 6 residues within 4Å: Chain A: P.27, L.29, F.49 Chain B: P.27, L.29, F.49 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 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.2, H2O.3 MG.9: 1 residues within 4Å: Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ATP.14 No protein-ligand interaction detected (PLIP) MG.11: 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.8, H2O.9, H2O.9

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 10 residues within 4Å: Chain A: K.56, S.83, S.84, G.85, N.86, H.87, R.135, N.154, G.239, S.242 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.84, A:G.85, A:N.86, A:H.87, A:R.135, A:N.154, A:S.242 Water bridges: A:R.135, A:G.186, A:S.242 Salt bridges: A:R.135 MLI.12: 10 residues within 4Å: Chain B: K.56, S.83, S.84, G.85, N.86, H.87, R.135, N.154, G.239, S.242 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.84, B:G.85, B:N.86, B:H.87, B:R.135, B:N.154, B:S.242 Water bridges: B:R.135 Salt bridges: B:R.135

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

EDO.4: 6 residues within 4Å: Chain A: P.130, S.131, D.132, R.135, K.241, S.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.130, A:D.132, A:R.135, A:S.242 Water bridges: A:K.241 EDO.5: 3 residues within 4Å: Chain A: E.264, D.265, K.268 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.264, A:K.268 EDO.6: 5 residues within 4Å: Chain A: N.213, N.229, L.230, Y.231, P.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.230, A:Y.231 Water bridges: A:N.213 EDO.15: 7 residues within 4Å: Chain B: P.130, S.131, D.132, R.135, K.241, S.242 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.130, B:D.132, B:R.135 Water bridges: B:K.241 EDO.16: 4 residues within 4Å: Chain B: S.212, D.215, Y.218, T.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.212, B:D.215, B:T.261 EDO.17: 4 residues within 4Å: Chain A: I.33 Chain B: A.120, Y.121 Ligands: ATP.14 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain B: E.264, D.265, K.268 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.265, B:K.268 GOL.8: 9 residues within 4Å: Chain B: S.84, P.107, P.130, S.131, D.132, R.135, K.241, S.242 Ligands: EDO.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.132, B:R.135 Water bridges: B:T.109, B:K.241, B:S.242, B:S.243

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.13: 16 residues within 4Å: Chain A: K.51, T.52, G.53, Q.89, A.117, A.120, Y.121, N.316 Chain B: T.30, S.31, S.32, I.33, E.276, R.277, K.279 Ligands: MG.9 20 PLIP interactions: 8 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:T.52, A:T.52, A:Q.89, B:S.31, B:S.32, B:I.33, B:R.277, B:R.277, B:K.279 Water bridges: A:H.24, A:K.51, B:T.30, B:T.30, B:T.30, B:T.30 Salt bridges: A:K.51, A:K.51, A:K.51 pi-Cation interactions: B:R.277, B:R.277 ATP.14: 17 residues within 4Å: Chain A: T.30, S.31, S.32, I.33, E.276, R.277, K.279 Chain B: H.24, K.51, T.52, G.53, Q.89, A.120, Y.121, N.316 Ligands: MG.10, EDO.17 25 PLIP interactions: 12 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:T.52, B:T.52, B:Q.89, B:N.316, A:S.31, A:S.32, A:I.33, A:K.279 Water bridges: B:H.24, B:H.24, B:K.51, B:K.51, A:T.30, A:T.30, A:T.30, A:T.30, A:S.32, A:S.32, A:R.277 Salt bridges: B:H.24, B:K.51, B:K.51, B:K.51 pi-Cation interactions: A:R.277, A:R.277

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
BBB

Serine racemase