Research workbench
Crystal structure of cytidine deaminase cdd from mycobacterium marinum
Analyse Crystal structure of cytidine deaminase cdd from mycobacterium marinum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F3W
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine deaminase cdd
- EC
- 3.5.4.5
- UniProt
- B2HDU6
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytidine deaminase cdd (EC 3.5.4.5) | protein | 119 | 34% helix, 22% strand | B2HDU6 |
| B | Cytidine deaminase cdd (EC 3.5.4.5) | protein | 121 | 34% helix, 23% strand | B2HDU6 |
| D | Cytidine deaminase cdd (EC 3.5.4.5) | protein | 120 | 36% helix, 23% strand | B2HDU6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.75 | 0.98 | 26 | empty |
| 2 | 207 | 0.63 | 0.83 | 27 | empty |
| 3 | 228 | 0.63 | 0.82 | 25 | ZN |
| 4 | 229 | 0.61 | 0.81 | 27 | empty |
| 5 | 237 | 0.61 | 0.80 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1053 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1044 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 472 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 447 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4F3W · Crystal structure of cytidine deaminase Cdd from Mycobacterium marinum · 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 B2HDU6
- Elsewhere: RCSB PDB 4F3W · PDBe 4F3W · UniProt B2HDU6
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