MolNFT v1 · #71184 · protein
Crystal structure of unknown function protein from leptospirillum rubarum
3M6J · Uncharacterized protein: “Crystal structure of unknown function protein from leptospirillum rubarum”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.62). MolNFT v1 #71184 on GenesisL1: 3D structure, binding sites…
- PDB
- 3M6J
- Type
- protein
- Length
- 526 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- Ligands
- CL
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 132 | 72% helix, 0% strand | — |
| B | Uncharacterized protein | protein | 126 | 71% helix, 0% strand | — |
| C | Uncharacterized protein | protein | 133 | 71% helix, 0% strand | — |
| D | Uncharacterized protein | protein | 135 | 67% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.62 | 0.78 | 47 | empty |
| 2 | 273 | 0.54 | 0.76 | 33 | empty |
| 3 | 107 | 0.48 | 0.80 | 14 | empty |
| 4 | 114 | 0.43 | 0.77 | 17 | empty |
| 5 | 127 | 0.40 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 736 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 728 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3M6J · Crystal structure of unknown function protein from Leptospirillum rubarum · 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
- Elsewhere: RCSB PDB 3M6J · PDBe 3M6J
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