Research workbench
Crystal structure of cytidine deaminase from mycobacterium smegmatis
Analyse Crystal structure of cytidine deaminase from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MPZ
- Type
- protein
- Length
- 491 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine deaminase
- EC
- 3.5.4.5
- UniProt
- A0QT11
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytidine deaminase (EC 3.5.4.5) | protein | 125 | 33% helix, 21% strand | A0QT11 |
| B | Cytidine deaminase (EC 3.5.4.5) | protein | 121 | 33% helix, 21% strand | A0QT11 |
| C | Cytidine deaminase (EC 3.5.4.5) | protein | 123 | 33% helix, 21% strand | A0QT11 |
| D | Cytidine deaminase (EC 3.5.4.5) | protein | 122 | 34% helix, 21% strand | A0QT11 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, 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 | 117 | 0.71 | 0.92 | 24 | empty |
| 2 | 116 | 0.70 | 0.91 | 27 | empty |
| 3 | 56 | 0.69 | 0.97 | 20 | empty |
| 4 | 95 | 0.68 | 0.92 | 24 | empty |
| 5 | 114 | 0.66 | 0.89 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1244 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1221 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 601 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 452 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3MPZ · Crystal structure of CYTIDINE DEAMINASE from Mycobacterium smegmatis · 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 A0QT11
- Elsewhere: RCSB PDB 3MPZ · PDBe 3MPZ · UniProt A0QT11
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