Research workbench
The crystal structure of bamb from moraxella catarrhalis
Analyse The crystal structure of bamb from moraxella catarrhalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IMM
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane assembly lipoprotein yfgl
- UniProt
- D5VCM9
- Ligands
- NA, CA, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane assembly lipoprotein yfgl | protein | 331 | 1% helix, 52% strand | D5VCM9 |
| B | Outer membrane assembly lipoprotein yfgl | protein | 322 | 0% helix, 53% strand | D5VCM9 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A
- CA · Calcium ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.70 | 0.76 | 88 | NA |
| 2 | 602 | 0.66 | 0.76 | 70 | CA |
| 3 | 92 | 0.59 | 0.88 | 22 | MG |
| 4 | 206 | 0.49 | 0.76 | 39 | empty |
| 5 | 81 | 0.37 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4IMM · The crystal structure of BamB from Moraxella catarrhalis · 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 D5VCM9
- Elsewhere: RCSB PDB 4IMM · PDBe 4IMM · UniProt D5VCM9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.