MolNFT v1 · #51728 · protein
RV2361 with ipp
2VG2 · Undecaprenyl pyrophosphate synthetase: “RV2361 with ipp”. X-ray diffraction, 4 ligands (DPO, IPE, PO4), 10 pockets (best druggability 0.82). MolNFT v1 #51728 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VG2
- Type
- protein
- Length
- 1,133 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
- DPO, IPE, PO4, CL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 283 | 41% helix, 14% strand | P60479 |
| C | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 283 | 41% helix, 14% strand | P60479 |
| D | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 284 | 42% helix, 14% strand | P60479 |
Ligands and binding sites
- DPO · Diphosphate · ligand · 3 copies · chains A, C, B, D
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, C, B, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, C, D
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 12 copies · chains A, B, D, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.82 | 0.84 | 89 | GOL, PO4 |
| 2 | 190 | 0.82 | 0.96 | 33 | DPO, IPE |
| 3 | 179 | 0.81 | 0.96 | 32 | DPO, IPE |
| 4 | 450 | 0.80 | 0.88 | 60 | DPO, PO4, GOL |
| 5 | 157 | 0.51 | 0.79 | 26 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2334 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2287 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 700 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 523 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2VG2 · Rv2361 with IPP · 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 2VG2 · PDBe 2VG2 · UniProt P60479
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