MolNFT v1 · #65821 · protein
RV0301 RV0300 toxin antitoxin complex from mycobacterium tuberculosis
3H87 · Putative uncharacterized protein: “RV0301 RV0300 toxin antitoxin complex from mycobacterium tuberculosis”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.58). MolNFT v1 #65821 on GenesisL1: 3D structure, binding…
- PDB
- 3H87
- Type
- protein
- Length
- 418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- O07228, O07227
- Ligands
- MG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 136 | 56% helix, 12% strand | O07228 |
| B | Putative uncharacterized protein | protein | 138 | 55% helix, 12% strand | O07228 |
| C, D | Putative uncharacterized protein | protein | 72 | 67% helix, 0% strand | O07227 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- BME · Beta-mercaptoethanol · additive · chains B
- IMD · Imidazole · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.58 | 0.82 | 33 | GOL |
| 2 | 87 | 0.38 | 0.77 | 19 | empty |
| 3 | 77 | 0.37 | 0.77 | 22 | empty |
| 4 | 51 | 0.25 | 0.73 | 15 | IMD |
Interfaces
6 interfaces between chains.
- B–C · 1665 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1536 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1214 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 344 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 341 Ų buried · 30 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 O07228
- Every structure of UniProt O07227
- Elsewhere: RCSB PDB 3H87 · PDBe 3H87 · UniProt O07228 · UniProt O07227
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