MolNFT v1 · #105608 · protein
Structure of vitamin B12 transporter btucd in a nucleotide-bound outward facing state
4R9U · Vitamin B12 import system permease protein btuc: “Structure of vitamin B12 transporter btucd in a nucleotide-bound outward facing state”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #105608…
- PDB
- 4R9U
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- 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
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vitamin B12 import system permease protein btuc (EC 3.6.3.33) | protein | 324 | 73% helix, 0% strand | P06609 |
| C, D | Vitamin B12 import ATP-binding protein btud (EC 3.6.3.33) | protein | 248 | 32% helix, 23% strand | P06611 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
- LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.86 | 0.90 | 58 | empty |
| 2 | 996 | 0.79 | 0.80 | 57 | empty |
| 3 | 1189 | 0.76 | 0.79 | 90 | ANP, MG |
| 4 | 1159 | 0.73 | 0.76 | 100 | empty |
| 5 | 328 | 0.69 | 0.83 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1571 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1540 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1043 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 964 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4R9U · Structure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.99
- 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 0.95
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 P06609
- Every structure of UniProt P06611
- Elsewhere: RCSB PDB 4R9U · PDBe 4R9U · UniProt P06609 · UniProt P06611
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