MolNFT v1 · #170162 · protein
NBE-LBM
6XYM: “NBE-LBM”. X-ray diffraction, 1 ligand (TB), 3 pockets (best druggability 0.64). MolNFT v1 #170162 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XYM
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nbe-lbm
- Ligands
- TB
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nbe-lbm | protein | 137 | 9% helix, 46% strand | — |
| B | Nbe-lbm | protein | 133 | 10% helix, 46% strand | — |
Ligands and binding sites
- TB · Terbium(iii) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.64 | 0.82 | 42 | empty |
| 2 | 139 | 0.50 | 0.79 | 19 | empty |
| 3 | 93 | 0.49 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 759 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6XYM · Nbe-LBM · 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 6XYM · PDBe 6XYM
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