SMTL ID : 2q16.1

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: E.61 Ligands: ITT.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, H2O.8, H2O.9 CA.7: 2 residues within 4Å: Chain B: E.61 Ligands: ITT.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.61, B:E.61, H2O.14

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

NA.2: 4 residues within 4Å: Chain A: N.30, D.115, F.174 Ligands: ITT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.30 Water bridges: A:N.30, A:D.115 NA.3: 5 residues within 4Å: Chain A: I.103, Y.104, S.105, A.106 Ligands: ITT.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.105, A:A.106 Water bridges: A:E.61, A:S.90, A:I.103, A:I.103, A:Y.104 NA.4: 6 residues within 4Å: Chain A: E.36, K.197, S.198, S.201, R.203, G.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.36, A:S.201, A:G.204 NA.8: 5 residues within 4Å: Chain B: N.30, D.115, F.174 Ligands: NA.9, ITT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.30 NA.9: 5 residues within 4Å: Chain B: D.115, N.118, Y.176 Ligands: NA.8, ITT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.118

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

SO4.5: 1 residues within 4Å: Chain A: R.215 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.215

2 x ITT: INOSINE 5'-TRIPHOSPHATE(Non-covalent)

ITT.6: 23 residues within 4Å: Chain A: T.28, G.29, N.30, K.33, E.61, K.73, D.88, A.89, S.90, G.91, S.105, A.106, F.138, F.174, G.175, Y.176, D.177, K.197, H.202, R.203 Ligands: CA.1, NA.2, NA.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.29, A:N.30, A:D.88, A:S.90, A:S.90, A:S.105, A:D.115, A:Y.176, A:K.197, A:H.202, A:R.203, A:R.203 Water bridges: A:S.58, A:D.115, A:N.118 Salt bridges: A:K.33, A:K.33, A:K.33, A:K.73, A:K.73, A:K.73 ITT.10: 23 residues within 4Å: Chain B: T.28, G.29, N.30, K.33, E.61, K.73, D.88, A.89, S.90, G.91, S.105, A.106, F.138, F.174, G.175, Y.176, D.177, K.197, H.202, R.203 Ligands: CA.7, NA.8, NA.9 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:T.28, B:G.29, B:N.30, B:N.30, B:D.88, B:S.90, B:S.90, B:S.105, B:D.115, B:Y.176, B:K.197, B:H.202, B:R.203, B:R.203 Water bridges: B:K.73, B:K.73, B:A.106 Salt bridges: B:K.33, B:K.33, B:K.33, B:K.73, B:K.73, B:K.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Savchenko, A. et al., Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli. J.Mol.Biol. (2007)

Release Date

2008-02-19

Peptides

HAM1 protein homolog: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HAM1 protein homolog

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