MolNFT v1 · #51520 · protein
E138D variant of escherichia COLI dctp deaminase in complex with dutp
2V9X · Deoxycytidine triphosphate deaminase: “E138D variant of escherichia COLI dctp deaminase in complex with dutp”. X-ray diffraction, 3 ligands (DUT, MG, SO4), 20 pockets (best druggability 0.88). MolNFT v1 #51520 on GenesisL1: 3D…
- PDB
- 2V9X
- Type
- protein
- Length
- 2,265 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine triphosphate deaminase
- EC
- 3.5.4.13
- UniProt
- P28248
- Ligands
- DUT, MG, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, K | Deoxycytidine triphosphate deaminase (EC 3.5.4.13) | protein | 193 | 19% helix, 35% strand | P28248 |
| J | Deoxycytidine triphosphate deaminase (EC 3.5.4.13) | protein | 161 | 12% helix, 41% strand | P28248 |
| L | Deoxycytidine triphosphate deaminase (EC 3.5.4.13) | protein | 174 | 16% helix, 39% strand | P28248 |
Ligands and binding sites
- DUT · Deoxyuridine-5'-triphosphate · ligand · 12 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- MG · Magnesium ion · metal · 12 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.88 | 0.90 | 116 | empty |
| 2 | 1189 | 0.88 | 0.89 | 109 | empty |
| 3 | 198 | 0.81 | 0.95 | 36 | DUT, MG |
| 4 | 191 | 0.80 | 0.95 | 34 | DUT, MG |
| 5 | 197 | 0.80 | 0.95 | 36 | DUT, MG |
Interfaces
33 interfaces between chains.
- J–K · 2021 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2012 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 2000 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1999 Ų buried · 33 hydrogen bonds · protein-protein
- G–I · 1999 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2V9X · E138D variant of Escherichia coli dCTP deaminase in complex with dUTP · the same entry in another collection · chain L against L, 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 P28248
- Elsewhere: RCSB PDB 2V9X · PDBe 2V9X · UniProt P28248
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