SMTL ID : 4r7w.1 (3 other biounits)

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with phosphonocytosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 6 residues within 4Å: Chain A: H.56, H.58, H.209, H.241, D.308 Ligands: O7U.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.56, A:H.58, A:H.209, A:D.308 FE2.6: 6 residues within 4Å: Chain B: H.56, H.58, H.209, H.241, D.308 Ligands: O7U.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.56, B:H.58, B:H.209, B:D.308

2 x O7U: (2R)-2-amino-2,5-dihydro-1,5,2-diazaphosphinin-6(1H)-one 2-oxide(Non-covalent)

O7U.2: 13 residues within 4Å: Chain A: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, L.277, D.308, W.314 Ligands: FE2.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.151, A:Q.151, A:E.212, A:E.212 O7U.7: 13 residues within 4Å: Chain B: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, L.277, D.308, W.314 Ligands: FE2.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.151, B:Q.151, B:E.212, B:E.212, B:E.273 Water bridges: B:E.212

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 8 residues within 4Å: Chain A: T.272, D.327, A.328, H.331 Chain B: T.272, D.327, A.328, H.331 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.331, A:D.327, A:H.331

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

EDO.4: 4 residues within 4Å: Chain A: D.214, P.216, R.287 Chain B: P.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.287, A:R.287 EDO.5: 5 residues within 4Å: Chain A: D.376, R.386, Q.387, A.388, R.389 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.376, A:D.376, A:R.386, A:R.386, A:R.389 EDO.8: 3 residues within 4Å: Chain B: S.254, F.257, R.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.254, B:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with phosphonocytosine. To be Published

Release Date

2014-09-17

Peptides

Cytosine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytosine deaminase

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