SMTL ID : 8xzc.1

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2) Tyr314Phe mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: E.182, E.183, E.221, R.294, F.332, S.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.183 Water bridges: A:G.185 PO4.2: 1 residues within 4Å: Chain A: E.47 No protein-ligand interaction detected (PLIP) PO4.5: 6 residues within 4Å: Chain B: E.182, E.183, E.221, R.294, F.332, S.369 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.183 Water bridges: B:G.185 PO4.6: 1 residues within 4Å: Chain B: E.47 No protein-ligand interaction detected (PLIP) PO4.9: 6 residues within 4Å: Chain C: E.182, E.183, E.221, R.294, F.332, S.369 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.183 Water bridges: C:G.185 PO4.10: 1 residues within 4Å: Chain C: E.47 No protein-ligand interaction detected (PLIP) PO4.13: 6 residues within 4Å: Chain D: E.182, E.183, E.221, R.294, F.332, S.369 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.183 Water bridges: D:G.185 PO4.14: 1 residues within 4Å: Chain D: E.47 No protein-ligand interaction detected (PLIP)

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.142, H.144, E.182, E.183, H.395 Ligands: ZN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.142, A:E.183, A:H.395, H2O.1 ZN.4: 6 residues within 4Å: Chain A: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.142, A:H.144, A:H.207, H2O.1, H2O.1 ZN.7: 6 residues within 4Å: Chain B: C.142, H.144, E.182, E.183, H.395 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.142, B:E.183, B:H.395, H2O.5 ZN.8: 6 residues within 4Å: Chain B: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.142, B:H.144, B:H.207, H2O.4, H2O.5 ZN.11: 6 residues within 4Å: Chain C: C.142, H.144, E.182, E.183, H.395 Ligands: ZN.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.142, C:E.183, C:H.395, H2O.8 ZN.12: 6 residues within 4Å: Chain C: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.142, C:H.144, C:H.207, H2O.8, H2O.8 ZN.15: 6 residues within 4Å: Chain D: C.142, H.144, E.182, E.183, H.395 Ligands: ZN.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.142, D:E.183, D:H.395, H2O.11 ZN.16: 6 residues within 4Å: Chain D: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:C.142, D:H.144, D:H.207, H2O.11, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandravanshi, K. et al., Crystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2) Tyr314Phe mutant. To Be Published

Release Date

2025-01-22

Peptides

Xaa-Arg dipeptidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xaa-Arg dipeptidase