SMTL ID : 5y4a.1

Cadmium directed assembly of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: T.117, I.120, Q.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.120 NA.7: 2 residues within 4Å: Chain B: T.117, I.120 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.120

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

SO4.2: 5 residues within 4Å: Chain A: E.68, A.69, R.70, K.91 Chain B: R.90 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.69, A:R.70 Water bridges: A:R.70, A:G.71, A:D.131 Salt bridges: A:R.70, A:K.91, B:R.90, B:K.94 SO4.3: 7 residues within 4Å: Chain A: L.133, A.134, T.135, G.136, G.137, T.138, I.139 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.134, A:A.134, A:G.136, A:G.137, A:T.138, A:T.138, A:T.138, A:I.139 SO4.8: 5 residues within 4Å: Chain A: R.90 Chain B: E.68, A.69, R.70, K.91 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.68, B:A.69, B:R.70 Water bridges: B:R.70, B:R.70, B:G.71 Salt bridges: B:R.70, B:K.91, A:R.90

5 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: D.130, D.131 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.130, A:D.131, H2O.1, H2O.1, H2O.1 CD.5: 1 residues within 4Å: Chain A: E.102 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.102, A:E.102 CD.6: 2 residues within 4Å: Chain B: E.54, E.58 No protein-ligand interaction detected (PLIP) CD.9: 3 residues within 4Å: Chain B: T.67, D.130, D.131 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.130, B:D.131, H2O.2, H2O.2, H2O.2 CD.10: 2 residues within 4Å: Chain B: H.155, H.177 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.155, B:H.177, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pavithra, G.C. et al., Cadmium directed assembly of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis. To be published

Release Date

2018-08-08

Peptides

Adenine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenine phosphoribosyltransferase

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