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Crystal structure of 5-methylcytosine deaminase from klebsiella pneumoniae liganded with phosphonocytosine
Analyse Crystal structure of 5-methylcytosine deaminase from klebsiella pneumoniae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R7W
- Type
- protein
- Length
- 2,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosine deaminase
- EC
- 3.5.4.1
- UniProt
- W8V4R8
- Ligands
- O7U, FE2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Cytosine deaminase (EC 3.5.4.1) | protein | 411 | 38% helix, 21% strand | W8V4R8 |
| B, D | Cytosine deaminase (EC 3.5.4.1) | protein | 412 | 37% helix, 21% strand | W8V4R8 |
| E | Cytosine deaminase (EC 3.5.4.1) | protein | 410 | 38% helix, 22% strand | W8V4R8 |
Ligands and binding sites
- O7U · (2R)-2-amino-2,5-dihydro-1,5,2-diazaphosphinin-6(1H)-one 2-oxide · ligand · 6 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D, F, C, E
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, E, D, F
- GOL · Glycerol · additive · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.85 | 0.93 | 51 | PEG |
| 2 | 401 | 0.84 | 0.92 | 50 | empty |
| 3 | 525 | 0.79 | 0.86 | 53 | PEG |
| 4 | 569 | 0.78 | 0.84 | 55 | PEG, EDO |
| 5 | 596 | 0.76 | 0.83 | 58 | PEG, EDO |
Interfaces
12 interfaces between chains.
- C–E · 2650 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2568 Ų buried · 52 hydrogen bonds · protein-protein
- D–F · 2552 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 796 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 794 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4R7W · Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt W8V4R8
- Elsewhere: RCSB PDB 4R7W · PDBe 4R7W · UniProt W8V4R8
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