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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: N.176, H.180 Chain B: R.113, H.115, S.119 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.119, B:S.119 Water bridges: B:A.120, A:A.120, A:A.120, A:N.176, A:N.176 Salt bridges: B:R.113, B:H.115, A:H.180 SO4.2: 3 residues within 4Å: Chain A: G.52, H.53, S.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.53, A:S.56 Salt bridges: A:H.53 SO4.6: 5 residues within 4Å: Chain A: R.113, H.115, S.119 Chain B: N.176, H.180 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Water bridges: B:A.120, B:A.120, B:N.176, B:N.176, A:A.120 Salt bridges: B:H.180, A:R.113, A:H.115 Hydrogen bonds: A:S.119, A:S.119 SO4.7: 3 residues within 4Å: Chain B: G.52, H.53, S.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.53, B:S.56 Salt bridges: B:H.53

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

NA.3: 5 residues within 4Å: Chain A: P.78, G.87, F.89, D.90 Ligands: APR.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.87, A:F.89, A:D.90 NA.8: 5 residues within 4Å: Chain B: P.78, G.87, F.89, D.90 Ligands: APR.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.78, B:F.89, B:D.90

2 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.4: 28 residues within 4Å: Chain A: D.23, T.24, N.25, G.52, H.53, L.54, Q.55, P.78, G.79, N.80, Y.84, G.87, G.88, F.89, D.90, A.92, T.148, V.149, P.152, P.191, G.192, C.194, T.195, G.196, Y.197, A.198 Ligands: NA.3, EDO.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.24, A:T.24, A:T.24, A:L.54, A:Q.55, A:N.80, A:G.87, A:F.89, A:C.194, A:C.194, A:T.195, A:G.196, A:Y.197, A:A.198 Water bridges: A:N.80, A:G.87, A:A.92, A:A.92, A:T.195, A:T.195 pi-Stacking: A:F.89 APR.9: 28 residues within 4Å: Chain B: D.23, T.24, N.25, G.52, H.53, L.54, Q.55, P.78, G.79, N.80, Y.84, G.87, G.88, F.89, D.90, A.92, T.148, V.149, P.152, P.191, G.192, C.194, T.195, G.196, Y.197, A.198 Ligands: NA.8, EDO.10 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:T.24, B:T.24, B:L.54, B:Q.55, B:N.80, B:G.87, B:F.89, B:D.90, B:T.148, B:C.194, B:C.194, B:G.196, B:Y.197, B:A.198 Water bridges: B:N.80, B:G.87, B:A.92, B:A.92, B:T.195, B:T.195 pi-Stacking: B:F.89

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

EDO.5: 6 residues within 4Å: Chain A: G.86, G.87, P.152, Y.197 Chain B: F.239 Ligands: APR.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.86, A:G.87 EDO.10: 6 residues within 4Å: Chain A: F.239 Chain B: G.86, G.87, P.152, Y.197 Ligands: APR.9 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.86, B:G.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumaran, D. et al., Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme. Protein Sci. (2005)

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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