SMTL ID : 4r88.1 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 1LD: 5-fluorocytosine(Non-covalent)

1LD.1: 14 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, S.309, W.314 Ligands: FE2.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.151, A:Q.151, A:E.212, A:E.273 Water bridges: A:E.212, A:E.212 1LD.13: 13 residues within 4Å: Chain B: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, E.273, L.277, D.308, S.309, W.314 Ligands: FE2.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.151, B:Q.151, B:E.212

2 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: 1LD.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 FE2.14: 6 residues within 4Å: Chain B: H.56, H.58, H.209, H.241, D.308 Ligands: 1LD.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.56, B:H.58, B:H.209, B:D.308

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.185, Q.217, S.218, R.219, F.220, E.222, V.223 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.185, A:R.219, A:E.222, A:E.222 Water bridges: A:Q.217 GOL.4: 6 residues within 4Å: Chain A: D.327, A.328 Chain B: R.324, D.327, A.328, H.331 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.324, B:D.327, A:D.327 GOL.7: 8 residues within 4Å: Chain A: D.282, P.285, K.286, R.287 Chain B: D.282, P.285, K.286, R.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.287, B:R.287 GOL.8: 6 residues within 4Å: Chain A: C.253, S.254, F.257, R.292, E.295 Chain B: W.284 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.284, A:R.292 GOL.15: 8 residues within 4Å: Chain B: R.185, V.189, Q.217, R.219, F.220, E.222, V.223 Ligands: PEG.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.185, B:R.219 Water bridges: B:E.222 GOL.18: 5 residues within 4Å: Chain A: W.70 Chain B: Y.338, L.341, Q.342, Y.381 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.338

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 6 residues within 4Å: Chain A: H.113, D.143, N.361, P.369, N.371, H.396 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.361 Hydrogen bonds: A:D.143, A:N.371 Salt bridges: A:R.395, A:H.396 ACY.6: 4 residues within 4Å: Chain A: E.137, A.138, D.140, L.141 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.137 ACY.16: 4 residues within 4Å: Chain B: S.254, F.257, R.292, E.295 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.257, B:E.295 Water bridges: B:R.292, B:R.292, A:W.284 Salt bridges: B:R.292

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

EDO.9: 5 residues within 4Å: Chain A: R.161, S.190, M.193, F.194, D.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.161, A:R.161, A:D.197, A:D.197 EDO.10: 2 residues within 4Å: Chain A: S.156, N.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156, A:N.183 EDO.11: 5 residues within 4Å: Chain A: R.46, D.376, A.377, E.378, R.386 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.376, A:R.386 EDO.12: 6 residues within 4Å: Chain A: D.42, A.43, R.46, L.391, T.392, Q.402 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.43, A:R.46, A:T.392, A:T.392, A:Q.402 EDO.19: 5 residues within 4Å: Chain B: D.143, P.369, N.371, R.395, H.396 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.371, B:R.395 EDO.20: 2 residues within 4Å: Chain B: Y.181, N.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.181, B:N.183 Water bridges: B:Y.181 EDO.21: 2 residues within 4Å: Chain B: R.229, V.230 No protein-ligand interaction detected (PLIP) EDO.22: 3 residues within 4Å: Chain B: G.171, D.173, R.204 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.171 EDO.23: 2 residues within 4Å: Chain B: R.201, Y.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.201

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

PEG.17: 8 residues within 4Å: Chain B: H.180, R.185, I.213, D.215, Q.217, S.218, F.220 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.217

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-fluorocytosine. 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

Related Entries With Identical Sequence