SMTL ID : 4r85.4 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x 17E: 5-methylcytosine(Non-covalent)

17E.1: 13 residues within 4Å: Chain A: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.314, A:W.314 Hydrogen bonds: A:Q.151, A:Q.151, A:E.212, A:E.273 Water bridges: A:E.212, A:E.212 17E.6: 13 residues within 4Å: Chain B: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.314, B:W.314 Hydrogen bonds: B:Q.151, B:Q.151, B:E.212 17E.12: 13 residues within 4Å: Chain C: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.13 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.314, C:W.314 Hydrogen bonds: C:Q.151, C:Q.151, C:E.212 17E.17: 13 residues within 4Å: Chain D: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.18 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.314, D:W.314 Hydrogen bonds: D:Q.151, D:Q.151, D:E.212 Water bridges: D:E.212, D:E.212 17E.21: 13 residues within 4Å: Chain E: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.22 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.314, E:W.314 Hydrogen bonds: E:Q.151, E:Q.151, E:E.212 17E.27: 13 residues within 4Å: Chain F: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.28 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:W.314, F:W.314 Hydrogen bonds: F:Q.151, F:Q.151, F:E.212, F:E.273 Water bridges: F:E.212, F:E.212 pi-Cation interactions: F:H.209

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

FE2.2: 6 residues within 4Å: Chain A: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.56, A:H.58, A:H.209, A:H.241, A:D.308 FE2.7: 6 residues within 4Å: Chain B: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.56, B:H.58, B:H.209, B:H.241, B:D.308 FE2.13: 6 residues within 4Å: Chain C: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.12 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.56, C:H.58, C:H.209, C:H.241, C:D.308 FE2.18: 6 residues within 4Å: Chain D: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.17 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.56, D:H.58, D:H.209, D:H.241, D:D.308 FE2.22: 6 residues within 4Å: Chain E: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.21 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.56, E:H.58, E:H.209, E:H.241, E:D.308 FE2.28: 6 residues within 4Å: Chain F: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.27 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.56, F:H.58, F:H.209, F:H.241, F:D.308

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: R.185, V.189, Q.217, S.218, R.219, F.220, E.222, V.223 Chain B: R.185 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: P.123, L.125, R.166 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: D.327, A.328, H.331 Chain D: D.327, A.328 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain B: P.92, E.93, R.96, A.130 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain B: S.254, F.257, R.292, E.295 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain B: R.185, V.189, Q.217, S.218, R.219, F.220, E.222, V.223 Chain C: R.185 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain B: Q.145, D.173, L.205, L.356, C.357 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain C: D.327, A.328 Chain E: D.327, A.328, H.331 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain A: R.185 Chain C: R.185, Q.217, S.218, R.219, F.220, E.222, V.223 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain C: C.253, S.254, F.257, R.292, E.295 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: W.284 Chain D: C.253, S.254, F.257, R.292, E.295 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain D: R.185, Q.217, S.218, R.219, F.220, E.222, V.223 Chain E: R.185 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain E: R.185, V.189, Q.217, S.218, R.219, F.220, E.222, V.223 Chain F: R.185 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain E: C.253, S.254, F.257, R.292, E.295 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain E: H.113, D.143, N.361, P.369, N.371, R.395, H.396 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain B: R.324, D.327, A.328, H.331 Chain F: D.327, A.328 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain D: R.185 Chain F: R.185, V.189, Q.217, S.218, R.219, F.220, E.222, V.223 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain B: W.284 Chain F: S.254, F.257, R.292, E.295 Ligand excluded by PLIP

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 5-methylcytosine. 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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