Research workbench
Crystal structure of adenine deaminase from agrobacterium tumefaciens (str. C 58)
Analyse Crystal structure of adenine deaminase from agrobacterium tumefaciens (str. C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NQB
- Type
- protein
- Length
- 1,174 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine deaminase 2
- EC
- 3.5.4.2
- UniProt
- Q7CUX4
- Ligands
- MN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine deaminase 2 (EC 3.5.4.2) | protein | 587 | 30% helix, 28% strand | Q7CUX4 |
| B | Adenine deaminase 2 (EC 3.5.4.2) | protein | 587 | 30% helix, 28% strand | Q7CUX4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.78 | 0.82 | 83 | empty |
| 2 | 693 | 0.77 | 0.82 | 81 | empty |
| 3 | 1002 | 0.77 | 0.79 | 75 | empty |
| 4 | 198 | 0.45 | 0.74 | 25 | empty |
| 5 | 166 | 0.41 | 0.73 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 395 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3NQB · Crystal Structure of Adenine Deaminase from Agrobacterium tumefaciens (str. C 58) · the same entry in another collection · chain B against B, TM-score 1.00
- Q7CUX4 · AlphaFold monomer V2.0 prediction for adenine deaminase 2 (Q7CUX4) · a predicted model of the same protein · chain B 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 Q7CUX4
- Elsewhere: RCSB PDB 3NQB · PDBe 3NQB · UniProt Q7CUX4
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