SMTL ID : 3o7u.1

Crystal structure of Cytosine Deaminase from Escherichia Coli complexed with zinc and phosphono-cytosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-hexamer

Ligands

6 x PXN: (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol(Non-covalent)

PXN.1: 8 residues within 4Å: Chain A: D.99, Q.103, W.106, Q.107, K.110, E.143 Chain F: L.417, E.418 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain A Hydrophobic interactions: F:E.418, A:K.110, A:E.143 Hydrogen bonds: A:Q.103, A:K.110 PXN.13: 8 residues within 4Å: Chain B: D.99, Q.103, W.106, Q.107, K.110, E.143 Chain E: L.417, E.418 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:K.110, B:E.143, E:E.418 Hydrogen bonds: B:Q.103, B:K.110 PXN.25: 8 residues within 4Å: Chain C: D.99, Q.103, W.106, Q.107, K.110, E.143 Chain D: L.417, E.418 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:K.110, C:E.143, D:E.418 Hydrogen bonds: C:Q.103, C:K.110 PXN.37: 8 residues within 4Å: Chain C: L.417, E.418 Chain D: D.99, Q.103, W.106, Q.107, K.110, E.143 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.110, D:E.143, C:E.418 Hydrogen bonds: D:Q.103, D:K.110 PXN.49: 8 residues within 4Å: Chain B: L.417, E.418 Chain E: D.99, Q.103, W.106, Q.107, K.110, E.143 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:E.418, E:K.110, E:E.143 Hydrogen bonds: E:Q.103, E:K.110 PXN.61: 8 residues within 4Å: Chain A: L.417, E.418 Chain F: D.99, Q.103, W.106, Q.107, K.110, E.143 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain F Hydrophobic interactions: A:E.418, F:K.110, F:E.143 Hydrogen bonds: F:Q.103, F:K.110

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.62, H.64, H.215, H.247, D.314 Ligands: O7U.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.62, A:H.64, A:H.215, A:D.314 ZN.3: 2 residues within 4Å: Chain A: H.98, E.139 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.98, A:E.139, A:E.139 ZN.14: 6 residues within 4Å: Chain B: H.62, H.64, H.215, H.247, D.314 Ligands: O7U.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.62, B:H.64, B:H.215, B:D.314 ZN.15: 2 residues within 4Å: Chain B: H.98, E.139 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.98, B:E.139, B:E.139 ZN.26: 6 residues within 4Å: Chain C: H.62, H.64, H.215, H.247, D.314 Ligands: O7U.28 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.62, C:H.64, C:H.215, C:D.314 ZN.27: 2 residues within 4Å: Chain C: H.98, E.139 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.98, C:E.139, C:E.139 ZN.38: 6 residues within 4Å: Chain D: H.62, H.64, H.215, H.247, D.314 Ligands: O7U.40 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.62, D:H.64, D:H.215, D:D.314 ZN.39: 2 residues within 4Å: Chain D: H.98, E.139 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.98, D:E.139, D:E.139 ZN.50: 6 residues within 4Å: Chain E: H.62, H.64, H.215, H.247, D.314 Ligands: O7U.52 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.62, E:H.64, E:H.215, E:D.314 ZN.51: 2 residues within 4Å: Chain E: H.98, E.139 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.98, E:E.139, E:E.139 ZN.62: 6 residues within 4Å: Chain F: H.62, H.64, H.215, H.247, D.314 Ligands: O7U.64 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.62, F:H.64, F:H.215, F:D.314 ZN.63: 2 residues within 4Å: Chain F: H.98, E.139 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.98, F:E.139, F:E.139

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

O7U.4: 15 residues within 4Å: Chain A: H.62, H.64, L.82, F.155, Q.157, I.184, H.215, E.218, H.247, V.279, L.283, D.314, D.315, W.320 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.157, A:Q.157, A:E.218, A:E.218 Water bridges: A:E.218, A:E.218 O7U.16: 15 residues within 4Å: Chain B: H.62, H.64, L.82, F.155, Q.157, I.184, H.215, E.218, H.247, V.279, L.283, D.314, D.315, W.320 Ligands: ZN.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.157, B:Q.157, B:E.218, B:E.218 Water bridges: B:E.218, B:E.218 O7U.28: 15 residues within 4Å: Chain C: H.62, H.64, L.82, F.155, Q.157, I.184, H.215, E.218, H.247, V.279, L.283, D.314, D.315, W.320 Ligands: ZN.26 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.157, C:Q.157, C:E.218, C:E.218 Water bridges: C:E.218, C:E.218 O7U.40: 15 residues within 4Å: Chain D: H.62, H.64, L.82, F.155, Q.157, I.184, H.215, E.218, H.247, V.279, L.283, D.314, D.315, W.320 Ligands: ZN.38 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.157, D:Q.157, D:E.218, D:E.218 O7U.52: 15 residues within 4Å: Chain E: H.62, H.64, L.82, F.155, Q.157, I.184, H.215, E.218, H.247, V.279, L.283, D.314, D.315, W.320 Ligands: ZN.50 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.157, E:Q.157, E:E.218, E:E.218 O7U.64: 15 residues within 4Å: Chain F: H.62, H.64, L.82, F.155, Q.157, I.184, H.215, E.218, H.247, V.279, L.283, D.314, D.315, W.320 Ligands: ZN.62 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.157, F:Q.157, F:E.218, F:E.218

36 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: H.235, H.236 Chain B: L.161, S.162, Y.163, P.164, F.189 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: R.391, D.424, Y.425 Chain F: T.325 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: Q.346, D.349, N.352, L.353 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: T.259, S.260, F.263 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: Q.206, D.209, R.242 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: E.50, Q.51, G.52, P.381, A.382, E.383, R.391, K.426 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain B: H.235, H.236 Chain C: L.161, S.162, Y.163, P.164, F.189 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: R.391, D.424, Y.425 Chain E: T.325 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: Q.346, D.349, N.352, L.353 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain B: T.259, S.260, F.263 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain B: Q.206, D.209, R.242 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: E.50, Q.51, G.52, P.381, A.382, E.383, R.391, K.426 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain A: L.161, S.162, Y.163, P.164, F.189 Chain C: H.235, H.236 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain C: R.391, D.424, Y.425 Chain D: T.325 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain C: Q.346, D.349, N.352, L.353 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain C: T.259, S.260, F.263 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain C: Q.206, D.209, R.242 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain C: E.50, Q.51, G.52, P.381, A.382, E.383, R.391, K.426 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain D: H.235, H.236 Chain E: L.161, S.162, Y.163, P.164, F.189 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain C: T.325 Chain D: R.391, D.424, Y.425 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain D: Q.346, D.349, N.352, L.353 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain D: T.259, S.260, F.263 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain D: Q.206, D.209, R.242 Ligand excluded by PLIP GOL.46: 8 residues within 4Å: Chain D: E.50, Q.51, G.52, P.381, A.382, E.383, R.391, K.426 Ligand excluded by PLIP GOL.53: 7 residues within 4Å: Chain E: H.235, H.236 Chain F: L.161, S.162, Y.163, P.164, F.189 Ligand excluded by PLIP GOL.54: 4 residues within 4Å: Chain B: T.325 Chain E: R.391, D.424, Y.425 Ligand excluded by PLIP GOL.55: 4 residues within 4Å: Chain E: Q.346, D.349, N.352, L.353 Ligand excluded by PLIP GOL.56: 3 residues within 4Å: Chain E: T.259, S.260, F.263 Ligand excluded by PLIP GOL.57: 3 residues within 4Å: Chain E: Q.206, D.209, R.242 Ligand excluded by PLIP GOL.58: 8 residues within 4Å: Chain E: E.50, Q.51, G.52, P.381, A.382, E.383, R.391, K.426 Ligand excluded by PLIP GOL.65: 7 residues within 4Å: Chain D: L.161, S.162, Y.163, P.164, F.189 Chain F: H.235, H.236 Ligand excluded by PLIP GOL.66: 4 residues within 4Å: Chain A: T.325 Chain F: R.391, D.424, Y.425 Ligand excluded by PLIP GOL.67: 4 residues within 4Å: Chain F: Q.346, D.349, N.352, L.353 Ligand excluded by PLIP GOL.68: 3 residues within 4Å: Chain F: T.259, S.260, F.263 Ligand excluded by PLIP GOL.69: 3 residues within 4Å: Chain F: Q.206, D.209, R.242 Ligand excluded by PLIP GOL.70: 8 residues within 4Å: Chain F: E.50, Q.51, G.52, P.381, A.382, E.383, R.391, K.426 Ligand excluded by PLIP

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

PEG.11: 2 residues within 4Å: Chain A: F.317 Chain F: R.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.69 PEG.12: 5 residues within 4Å: Chain A: Q.73, P.74, R.92, L.95, D.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.92, A:D.100 PEG.23: 2 residues within 4Å: Chain B: F.317 Chain E: R.390 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.69 PEG.24: 5 residues within 4Å: Chain B: Q.73, P.74, R.92, L.95, D.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.92, B:D.100 PEG.35: 2 residues within 4Å: Chain C: F.317 Chain D: R.390 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.69 PEG.36: 5 residues within 4Å: Chain C: Q.73, P.74, R.92, L.95, D.100 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.92, C:D.100 PEG.47: 2 residues within 4Å: Chain C: R.390 Chain D: F.317 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.69 PEG.48: 5 residues within 4Å: Chain D: Q.73, P.74, R.92, L.95, D.100 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.92, D:D.100 PEG.59: 2 residues within 4Å: Chain B: R.390 Chain E: F.317 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.69 PEG.60: 5 residues within 4Å: Chain E: Q.73, P.74, R.92, L.95, D.100 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.92, E:D.100 PEG.71: 2 residues within 4Å: Chain A: R.390 Chain F: F.317 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.69 PEG.72: 5 residues within 4Å: Chain F: Q.73, P.74, R.92, L.95, D.100 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.92, F:D.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hall, R.S. et al., Three-dimensional structure and catalytic mechanism of Cytosine deaminase. Biochemistry (2011)

Release Date

2011-06-15

Peptides

Cytosine deaminase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Cytosine deaminase

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