MolNFT v1 · #91598 · protein
Structure of vitamin B12 transporter btucd-F in a nucleotide-bound state
4FI3 · Vitamin B12 import system permease protein btuc: “Structure of vitamin B12 transporter btucd-F in a nucleotide-bound state”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #91598 on GenesisL1…
- PDB
- 4FI3
- Type
- protein
- Length
- 1,389 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 import system permease protein btuc; Vitamin B12 import ATP-binding protein…
- EC
- 3.6.3.33
- UniProt
- P06609, P06611, P37028
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vitamin B12 import system permease protein btuc | protein | 324 | 74% helix, 0% strand | P06609 |
| C, D | Vitamin B12 import ATP-binding protein btud (EC 3.6.3.33) | protein | 248 | 37% helix, 28% strand | P06611 |
| F | Vitamin B12-binding protein | protein | 245 | 42% helix, 14% strand | P37028 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.85 | 0.88 | 60 | empty |
| 2 | 1105 | 0.84 | 0.85 | 74 | empty |
| 3 | 530 | 0.79 | 0.86 | 66 | empty |
| 4 | 512 | 0.78 | 0.85 | 57 | empty |
| 5 | 140 | 0.77 | 0.95 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2063 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 1561 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1496 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 1281 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 975 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FI3 · Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state · the same entry in another collection · chain F against F, TM-score 1.00
- P06611 · AlphaFold monomer V2.0 prediction for vitamin B12 import ATP-binding protein btud (P06611) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P37028 · AlphaFold monomer V2.0 prediction for vitamin B12-binding protein (P37028) · a predicted model of the same protein · chain F against A, TM-score 0.97
- P06609 · AlphaFold monomer V2.0 prediction for vitamin B12 import system permease protein btuc… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P06609
- Every structure of UniProt P06611
- Every structure of UniProt P37028
- Elsewhere: RCSB PDB 4FI3 · PDBe 4FI3 · UniProt P06609 · UniProt P06611 · UniProt P37028
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