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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 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 FE2.9: 6 residues within 4Å: Chain C: H.56, H.58, H.209, H.241, D.308 Ligands: O7U.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.56, C:H.58, C:H.209, C:D.308 FE2.15: 6 residues within 4Å: Chain D: H.56, H.58, H.209, H.241, D.308 Ligands: O7U.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.56, D:H.58, D:H.209, D:D.308 FE2.19: 6 residues within 4Å: Chain E: H.56, H.58, H.209, H.241, D.308 Ligands: O7U.20 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.56, E:H.58, E:H.209, E:D.308 FE2.23: 6 residues within 4Å: Chain F: H.56, H.58, H.209, H.241, D.308 Ligands: O7U.24 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.56, F:H.58, F:H.209, F:D.308

6 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 O7U.10: 13 residues within 4Å: Chain C: 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: FE2.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.151, C:Q.151, C:E.212, C:E.212 O7U.16: 13 residues within 4Å: Chain D: 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: FE2.15 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.151, D:Q.151, D:E.212, D:E.212 pi-Stacking: D:H.209 O7U.20: 13 residues within 4Å: Chain E: 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: FE2.19 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:Q.151, E:Q.151, E:E.212, E:E.212, E:E.273 Water bridges: E:E.212, E:E.212 pi-Cation interactions: E:H.209 O7U.24: 13 residues within 4Å: Chain F: 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: FE2.23 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Q.151, F:Q.151, F:E.212, F:E.212, F:E.273 Water bridges: F:E.212, F:E.212 pi-Stacking: F:H.209, F:W.314, F:W.314

5 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: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.327, A:H.331, B:H.331 PEG.12: 7 residues within 4Å: Chain C: T.272, D.327, A.328, I.332 Chain E: D.327, A.328, H.331 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.327, C:D.327 PEG.13: 10 residues within 4Å: Chain A: K.255 Chain C: P.179, H.180, E.182, T.184, R.185, G.188, Q.217, S.218, F.220 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:E.182, C:E.182 Water bridges: C:Q.217, C:Q.217, C:R.219, A:R.219, A:K.255, A:K.255 PEG.17: 6 residues within 4Å: Chain D: D.327, A.328, H.331 Chain F: D.327, A.328, H.331 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:D.327, D:D.327 PEG.22: 5 residues within 4Å: Chain C: Y.338, Y.381 Chain E: A.65, W.70, Q.311 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.65

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

EDO.4: 5 residues within 4Å: Chain A: D.214, P.216, R.287 Chain B: P.285 Chain D: D.249 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.287, A:R.287, D:D.249, D:D.249 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: 5 residues within 4Å: Chain B: S.254, F.257, R.258 Chain F: F.77, E.78 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:S.254, B:R.258 Water bridges: F:F.77 EDO.14: 8 residues within 4Å: Chain C: R.389, E.404, V.405, E.406, H.407 Chain E: R.389, E.404, V.405 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:R.389, C:R.389, E:R.389, E:H.407, E:H.407 Water bridges: C:E.406, C:H.407 EDO.18: 4 residues within 4Å: Chain D: R.72, R.280 Chain F: R.298, H.334 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:R.298, D:R.280 Water bridges: F:R.298, F:H.334, F:H.334, F:G.337, D:R.72, D:R.280 EDO.21: 5 residues within 4Å: Chain C: Q.387 Chain E: N.319, N.321, R.324, Q.387 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.319, E:N.319, E:N.321, E:Q.387

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain C: C.253, S.254, F.257, R.292, E.295 Chain E: W.284 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:C.253, C:R.292, E:W.284 Water bridges: C:S.254

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Cytosine deaminase

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