MolNFT v1 · #52406 · protein
Crystal structure of RV0802C from mycobacterium tuberculosis in an unliganded form.
2VZY: “Crystal structure of RV0802C from mycobacterium tuberculosis in an unliganded form.”. X-ray diffraction, 3 ligands (ETX, SM, SO4), 15 pockets (best druggability 0.75). MolNFT v1 #52406 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VZY
- Type
- protein
- Length
- 763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RV0802C
- UniProt
- O06632
- Ligands
- ETX, SM, SO4
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RV0802C | protein | 192 | 40% helix, 35% strand | O06632 |
| B, D | RV0802C | protein | 191 | 38% helix, 35% strand | O06632 |
| C | RV0802C | protein | 189 | 39% helix, 36% strand | O06632 |
Ligands and binding sites
- ETX · 2-ethoxyethanol · ligand · 5 copies · chains A, B, C, D
- SM · Samarium (III) ion · metal · chains D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.75 | 0.98 | 22 | empty |
| 2 | 74 | 0.74 | 0.97 | 21 | empty |
| 3 | 274 | 0.52 | 0.75 | 41 | empty |
| 4 | 260 | 0.52 | 0.75 | 41 | empty |
| 5 | 161 | 0.44 | 0.75 | 26 | ACT, SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1057 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1038 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 795 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 773 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2VZY · Crystal structure of Rv0802c from Mycobacterium tuberculosis in an unliganded form. · 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 O06632
- Elsewhere: RCSB PDB 2VZY · PDBe 2VZY · UniProt O06632
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