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Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from agrobacterium tumefaciens
Analyse Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R9Q
- Type
- protein
- Length
- 1,346 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-deoxycytidine 5'-triphosphate deaminase; Synthetic peptide 1; Synthetic peptide 2
- UniProt
- Q8UI65
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-deoxycytidine 5'-triphosphate deaminase | protein | 327 | 12% helix, 43% strand | Q8UI65 |
| B | 2'-deoxycytidine 5'-triphosphate deaminase | protein | 342 | 11% helix, 42% strand | Q8UI65 |
| C | 2'-deoxycytidine 5'-triphosphate deaminase | protein | 331 | 11% helix, 43% strand | Q8UI65 |
| D | 2'-deoxycytidine 5'-triphosphate deaminase | protein | 330 | 11% helix, 45% strand | Q8UI65 |
| X | Synthetic peptide 1 | protein | 7 | 0% helix, 14% strand | — |
| Y | Synthetic peptide 2 | protein | 9 | 0% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.79 | 0.81 | 71 | empty |
| 2 | 618 | 0.79 | 0.84 | 67 | empty |
| 3 | 730 | 0.77 | 0.82 | 75 | empty |
| 4 | 1061 | 0.76 | 0.78 | 86 | empty |
| 5 | 184 | 0.64 | 0.84 | 24 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1359 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1303 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 592 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 7 hydrogen bonds · protein-protein
- B–Y · 543 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2R9Q · Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium… · 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 Q8UI65
- Elsewhere: RCSB PDB 2R9Q · PDBe 2R9Q · UniProt Q8UI65
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