MolNFT v1 · #159960 · protein
Structure of ybtpq importer with substrate ybt-fe bound
6P6J · Inner membrane ABC-transporter: “Structure of ybtpq importer with substrate ybt-fe bound”. Electron microscopy, 2 ligands (O34, FE), 20 pockets (best druggability 0.81). MolNFT v1 #159960 on GenesisL1: 3D structure, binding sites…
- PDB
- 6P6J
- Type
- protein
- Length
- 1,140 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inner membrane ABC-transporter; ABC transporter protein
- UniProt
- Q1RAG2, Q1RAG3
- Ligands
- O34, FE
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inner membrane ABC-transporter | protein | 571 | 60% helix, 8% strand | Q1RAG2 |
| B | ABC transporter protein | protein | 569 | 62% helix, 9% strand | Q1RAG3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.81 | 0.82 | 81 | empty |
| 2 | 838 | 0.80 | 0.83 | 70 | O34, FE |
| 3 | 641 | 0.72 | 0.79 | 87 | empty |
| 4 | 228 | 0.66 | 0.83 | 24 | empty |
| 5 | 98 | 0.61 | 0.88 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 7077 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6P6J · Structure of YbtPQ importer with substrate Ybt-Fe bound · the same entry in another collection · chain A against A, TM-score 1.00
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 Q1RAG2
- Every structure of UniProt Q1RAG3
- Elsewhere: RCSB PDB 6P6J · PDBe 6P6J · UniProt Q1RAG2 · UniProt Q1RAG3
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