MolNFT v1 · #51693 · protein
Aquifex aeolicus ispe in complex with ligand
2VF3 · 4-diphosphocytidyl-2C-methyl-D-erythritol kinase: “Aquifex aeolicus ispe in complex with ligand”. X-ray diffraction, 4 ligands (GVS, POP, CL), 3 pockets (best druggability 0.65). MolNFT v1 #51693 on GenesisL1: 3D structure, binding…
- PDB
- 2VF3
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-diphosphocytidyl-2C-methyl-D-erythritol kinase
- EC
- 2.7.1.148
- UniProt
- O67060
- Ligands
- GVS, POP, CL, BR
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 269 | 38% helix, 28% strand | O67060 |
| B | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 270 | 38% helix, 28% strand | O67060 |
Ligands and binding sites
- GVS · ethyl {3-[4-amino-5-{3-[(cyclopropylsulfonyl)amino]prop-1-yn-1-yl}-2-oxopyrimidin-1(2H)-yl]oxetan-3-yl}acetate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.65 | 0.79 | 41 | GVS, POP |
| 2 | 358 | 0.64 | 0.79 | 40 | GVS, POP, CL |
| 3 | 437 | 0.63 | 0.77 | 54 | CL, BR |
Interfaces
1 interface between chains.
- A–B · 395 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 O67060
- Elsewhere: RCSB PDB 2VF3 · PDBe 2VF3 · UniProt O67060
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