Research workbench
In meso crystal structure of the cobalamin transporter, btub
Analyse In meso crystal structure of the cobalamin transporter, btub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GUF
- Type
- protein
- Length
- 551 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 transporter btub
- UniProt
- P06129
- Ligands
- MPG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12 transporter btub | protein | 551 | 7% helix, 63% strand | P06129 |
Ligands and binding sites
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 11 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.82 | 0.86 | 94 | empty |
| 2 | 556 | 0.82 | 0.88 | 96 | MPD |
| 3 | 308 | 0.75 | 0.87 | 50 | empty |
| 4 | 70 | 0.74 | 0.99 | 32 | empty |
| 5 | 474 | 0.65 | 0.78 | 50 | FMT |
Compared structures
- 2GUF · In meso crystal structure of the cobalamin transporter, BtuB · 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 0.95
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 2GUF · PDBe 2GUF · UniProt P06129
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