Research workbench
Crystal structure of native MSMEG3575 deaminase from mycobacterium smegmatis
Analyse Crystal structure of native MSMEG3575 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
- 5XKO
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CYTIDINE/DEOXYCYTIDYLATE deaminase, zinc-binding region
- UniProt
- A0QY90
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CYTIDINE/DEOXYCYTIDYLATE deaminase, zinc-binding region | protein | 157 | 48% helix, 16% strand | A0QY90 |
| B | CYTIDINE/DEOXYCYTIDYLATE deaminase, zinc-binding region | protein | 158 | 50% helix, 16% strand | A0QY90 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.67 | 0.84 | 33 | CAC, GOL, ZN |
| 2 | 172 | 0.66 | 0.86 | 33 | CAC, GOL |
Interfaces
1 interface between chains.
- A–B · 1113 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5XKO · Crystal structure of native Msmeg3575 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 A0QY90
- Elsewhere: RCSB PDB 5XKO · PDBe 5XKO · UniProt A0QY90
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