Research workbench
Structure of a B12 binding lipoprotein from bacteroides thetaiotaomicron
Analyse Structure of a B12 binding lipoprotein from bacteroides thetaiotaomicron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BIZ
- Type
- protein
- Length
- 945 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface protein
- UniProt
- A0A0N7IAT3
- Ligands
- CNC, CA, NA
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell surface protein | protein | 478 | 5% helix, 41% strand | A0A0N7IAT3 |
| B | Cell surface protein | protein | 467 | 5% helix, 40% strand | A0A0N7IAT3 |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- 15P · Polyethylene glycol (N=34) · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.82 | 0.83 | 88 | empty |
| 2 | 385 | 0.81 | 0.90 | 42 | empty |
| 3 | 399 | 0.80 | 0.89 | 55 | empty |
| 4 | 340 | 0.62 | 0.79 | 47 | MES |
| 5 | 178 | 0.56 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1521 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7BIZ · Structure of a B12 binding lipoprotein from Bacteroides thetaiotaomicron · 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 A0A0N7IAT3
- Elsewhere: RCSB PDB 7BIZ · PDBe 7BIZ · UniProt A0A0N7IAT3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.