MolNFT v1 · #51729 · protein
RV2361 with citronellyl pyrophosphate
2VG3 · Undecaprenyl pyrophosphate synthetase: “RV2361 with citronellyl pyrophosphate”. X-ray diffraction, 5 ligands (GPP, MG, PO4), 10 pockets (best druggability 0.83). MolNFT v1 #51729 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2VG3
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthetase
- EC
- 2.5.1.31
- UniProt
- P60479
- Ligands
- GPP, MG, PO4, CL, SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 284 | 40% helix, 14% strand | P60479 |
| D | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 283 | 41% helix, 14% strand | P60479 |
Ligands and binding sites
- GPP · Geranyl diphosphate · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.83 | 0.84 | 104 | PO4, MG, GPP |
| 2 | 234 | 0.81 | 0.94 | 37 | MG, GPP, PO4 |
| 3 | 501 | 0.80 | 0.87 | 66 | MG, GPP |
| 4 | 249 | 0.80 | 0.93 | 35 | MG, GPP, PO4 |
| 5 | 105 | 0.45 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2228 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2227 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 685 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 473 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2VG3 · Rv2361 with citronellyl pyrophosphate · 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 P60479
- Elsewhere: RCSB PDB 2VG3 · PDBe 2VG3 · UniProt P60479
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