MolNFT v1 · #77489 · protein
Crystal structure of spin-labeled btub T156R1
3RGM · Vitamin B12 transporter btub: “Crystal structure of spin-labeled btub T156R1”. X-ray diffraction, 2 ligands (MTN, MG), 7 pockets (best druggability 0.86). MolNFT v1 #77489 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3RGM
- Type
- protein
- Length
- 548 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
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12 transporter btub | protein | 548 | 6% helix, 62% 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 · 9 copies · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 6 copies · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.86 | 0.90 | 98 | empty |
| 2 | 144 | 0.79 | 0.96 | 44 | empty |
| 3 | 63 | 0.71 | 0.98 | 32 | empty |
| 4 | 377 | 0.69 | 0.82 | 47 | empty |
| 5 | 465 | 0.67 | 0.79 | 51 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 3RGM · PDBe 3RGM · UniProt P06129
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