Research workbench
Crystal structure of spin-labeled btub V10R1 in the apo state
Analyse Crystal structure of spin-labeled btub V10R1 in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M8B
- Type
- protein
- Length
- 549 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 transporter btub
- UniProt
- P06129
- Ligands
- MTN, MG
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12 transporter btub | protein | 549 | 7% helix, 61% strand | P06129 |
Ligands and binding sites
- MTN · S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 7 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.85 | 0.86 | 125 | MTN |
| 2 | 152 | 0.80 | 0.96 | 41 | empty |
| 3 | 65 | 0.73 | 0.99 | 30 | empty |
| 4 | 476 | 0.70 | 0.81 | 49 | empty |
| 5 | 565 | 0.64 | 0.76 | 72 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3M8B · Crystal structure of spin-labeled BtuB V10R1 in the apo state · the same entry in another collection · chain A against A, TM-score 1.00
- P06129 · AlphaFold monomer V2.0 prediction for vitamin B12 transporter btub (P06129) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P06129
- Elsewhere: RCSB PDB 3M8B · PDBe 3M8B · UniProt P06129
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