Research workbench
Crystal structure of dcmp deaminase from the cyanophage S-TIM5 in complex with dtmp and dttp.
Analyse Crystal structure of dcmp deaminase from the cyanophage S-TIM5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P9D
- Type
- protein
- Length
- 811 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidylate deaminase
- UniProt
- H6WFU3
- Ligands
- TTP, TMP, ZN, MG, CL
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Deoxycytidylate deaminase | protein | 135 | 33% helix, 23% strand | H6WFU3 |
| C | Deoxycytidylate deaminase | protein | 136 | 33% helix, 24% strand | H6WFU3 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 6 copies · chains A, B, D, C, E, F
- TMP · Thymidine-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.73 | 0.79 | 76 | MG, TTP |
| 2 | 479 | 0.69 | 0.80 | 60 | TMP |
| 3 | 406 | 0.67 | 0.80 | 61 | TMP |
| 4 | 416 | 0.63 | 0.77 | 46 | MG, TTP |
| 5 | 162 | 0.58 | 0.82 | 30 | TMP |
Interfaces
6 interfaces between chains.
- A–D · 1273 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1269 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1225 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 839 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 793 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4P9D · Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dTMP and… · 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 H6WFU3
- Elsewhere: RCSB PDB 4P9D · PDBe 4P9D · UniProt H6WFU3
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