SMTL ID : 8wlw.1 (1 other biounit)

Crystal structure of DelP123_Msd in complex with 5-azauracil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

2 x WHC: 1~{H}-1,3,5-triazine-2,4-dione

WHC.1: 8 residues within 4Å: Chain A: F.28, N.45, H.55, P.56, E.57, C.85 Chain B: W.94 Ligands: ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.45, A:E.57 Water bridges: A:H.55, A:C.85 pi-Stacking: A:F.28, A:H.55 WHC.4: 8 residues within 4Å: Chain A: W.94 Chain B: F.28, N.45, H.55, P.56, E.57, C.85 Ligands: ZN.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.45, B:E.57 Water bridges: B:H.55, B:C.85 pi-Stacking: B:F.28, B:H.55

2 x GOL: GLYCEROL

GOL.2: 2 residues within 4Å: Chain A: A.123, T.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.124 Water bridges: A:V.122 GOL.5: 6 residues within 4Å: Chain B: L.16, E.19, E.42, D.43, R.44, R.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.43, B:R.46 Water bridges: B:R.44

2 x ZN: ZINC ION

ZN.3: 5 residues within 4Å: Chain A: H.55, E.57, C.85, C.88 Ligands: WHC.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.55, A:C.85, A:C.88, H2O.1 ZN.6: 5 residues within 4Å: Chain B: H.55, E.57, C.85, C.88 Ligands: WHC.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.55, B:C.85, B:C.88, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porathoor, S. et al., Crystal structure of DelP123_Msd in complex with 5-azauracil. To Be Published

Release Date

2024-09-18

Peptides

CMP/dCMP deaminase, zinc-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CMP/dCMP deaminase, zinc-binding protein

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