MolNFT v1 · #105553 · protein
Crystal structure of 5-methylcytosine deaminase from klebsiella pneumoniae liganded with 5-fluorocytosine
4R88: “Crystal structure of 5-methylcytosine deaminase from klebsiella pneumoniae liganded with 5-fluorocytosine”. X-ray diffraction, 2 ligands (1LD, FE2), 20 pockets (best druggability 0.85). MolNFT v1 #105553 on GenesisL1: 3D structure…
- PDB
- 4R88
- Type
- protein
- Length
- 2,469 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
- 1LD, FE2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Cytosine deaminase (EC 3.5.4.1) | protein | 411 | 39% helix, 21% strand | W8V4R8 |
| B | Cytosine deaminase (EC 3.5.4.1) | protein | 413 | 38% helix, 22% strand | W8V4R8 |
| D | Cytosine deaminase (EC 3.5.4.1) | protein | 412 | 38% helix, 23% strand | W8V4R8 |
Ligands and binding sites
- 1LD · 5-fluorocytosine · ligand · 6 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 18 copies · chains A, C, B, F, D, E
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, D, B, E, C
- ACY · Acetic acid · additive · 10 copies · chains A, B, C, E, D, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, E, D, F
- FLC · Citrate anion · additive · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.85 | 0.94 | 50 | GOL, PEG, ACY |
| 2 | 410 | 0.85 | 0.92 | 49 | GOL |
| 3 | 541 | 0.77 | 0.84 | 53 | GOL |
| 4 | 520 | 0.77 | 0.84 | 53 | PEG |
| 5 | 555 | 0.76 | 0.83 | 56 | GOL |
Interfaces
12 interfaces between chains.
- C–E · 2611 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2595 Ų buried · 46 hydrogen bonds · protein-protein
- D–F · 2552 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 829 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 823 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4R88 · 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 4R88 · PDBe 4R88 · UniProt W8V4R8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.