Research workbench
Crystal structure of cytidine deaminase from mycobacterium leprae
Analyse Crystal structure of cytidine deaminase from mycobacterium leprae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R2N
- Type
- protein
- Length
- 481 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine deaminase
- UniProt
- B8ZST1
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytidine deaminase | protein | 119 | 34% helix, 25% strand | B8ZST1 |
| B | Cytidine deaminase | protein | 121 | 36% helix, 25% strand | B8ZST1 |
| D | Cytidine deaminase | protein | 122 | 34% helix, 25% strand | B8ZST1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains 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 | 64 | 0.72 | 0.98 | 23 | empty |
| 2 | 214 | 0.62 | 0.82 | 26 | EDO |
| 3 | 196 | 0.61 | 0.82 | 24 | EDO |
| 4 | 196 | 0.61 | 0.82 | 26 | EDO |
| 5 | 193 | 0.60 | 0.82 | 25 | EDO |
Interfaces
6 interfaces between chains.
- A–D · 1035 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1029 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 456 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 452 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 445 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3R2N · Crystal structure of cytidine deaminase from Mycobacterium leprae · 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 B8ZST1
- Elsewhere: RCSB PDB 3R2N · PDBe 3R2N · UniProt B8ZST1
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