SMTL ID : 1ty8.1 (1 other biounit)

Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase, complexed with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: P.78, G.87, F.89, D.90 Ligands: ADP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.87, A:F.89, A:D.90 NA.2: 5 residues within 4Å: Chain A: P.78, G.79, T.148, V.149 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.148 NA.5: 5 residues within 4Å: Chain B: P.78, G.87, F.89, D.90 Ligands: ADP.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.87, B:F.89, B:D.90 Water bridges: B:D.90 NA.6: 5 residues within 4Å: Chain B: P.78, G.79, T.148, V.149 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.78

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: H.53, L.54, Q.55, A.92 Ligands: ADP.4 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: H.53, L.54, Q.55, A.92 Ligands: ADP.8 Ligand excluded by PLIP

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 22 residues within 4Å: Chain A: D.23, T.24, N.25, G.52, H.53, L.54, P.78, G.87, G.88, F.89, A.92, T.148, P.191, G.192, C.194, T.195, G.196, Y.197, A.198 Ligands: NA.1, NA.2, CL.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.24, A:T.24, A:H.53, A:L.54, A:F.89, A:T.148, A:C.194, A:C.194, A:T.195, A:T.195, A:G.196, A:Y.197, A:A.198 Water bridges: A:N.25, A:N.25, A:A.92, A:A.92, A:T.195 pi-Stacking: A:F.89 ADP.8: 22 residues within 4Å: Chain B: D.23, T.24, N.25, G.52, H.53, L.54, P.78, G.87, G.88, F.89, A.92, T.148, P.191, G.192, C.194, T.195, G.196, Y.197, A.198 Ligands: NA.5, NA.6, CL.7 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.24, B:H.53, B:L.54, B:F.89, B:T.148, B:C.194, B:C.194, B:T.195, B:G.196, B:Y.197, B:A.198 Water bridges: B:T.24, B:N.25, B:N.25, B:A.92, B:A.92, B:T.195 pi-Stacking: B:F.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumaran, D. et al., CRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YMX7. To be Published

Release Date

2004-11-30

Peptides

Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region

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