Research workbench
ABC-transporter btucd in complex with its periplasmic binding protein btuf
Analyse ABC-transporter btucd in complex with its periplasmic binding protein btuf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QI9
- 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
- SO4, PO4
- Pockets
- 20 · best druggability 0.87
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, 29% strand | P06611 |
| F | Vitamin B12-binding protein btuf | protein | 245 | 41% helix, 16% strand | P37028 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains C, D
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains C, D
- 1PE · Pentaethylene glycol · additive · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.87 | 0.88 | 111 | empty |
| 2 | 883 | 0.84 | 0.86 | 94 | PO4, 1PE |
| 3 | 1138 | 0.82 | 0.83 | 104 | empty |
| 4 | 532 | 0.69 | 0.79 | 63 | empty |
| 5 | 276 | 0.60 | 0.79 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1903 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 1424 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1353 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1174 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1163 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 2QI9 · ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF · 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 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 0.99
- 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
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 2QI9 · PDBe 2QI9 · UniProt P06609 · UniProt P06611 · UniProt P37028
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