Research workbench
ABC transporter nosdfy E154Q, ATP-bound in lipid nanodisc
Analyse ABC transporter nosdfy E154Q, ATP-bound in lipid nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O17
- Type
- protein
- Length
- 1,531 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ABC transporter binding protein nosd; Probable ABC transporter ATP-binding…
- UniProt
- P19843, P19844, P19845
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ABC transporter binding protein nosd | protein | 403 | 7% helix, 34% strand | P19843 |
| B, C | Probable ABC transporter ATP-binding protein nosf | protein | 298 | 30% helix, 19% strand | P19844 |
| D | Probable ABC transporter permease protein nosy | protein | 273 | 67% helix, 0% strand | P19845 |
| E | Probable ABC transporter permease protein nosy | protein | 259 | 63% helix, 0% strand | P19845 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.86 | 0.91 | 73 | empty |
| 2 | 168 | 0.83 | 0.97 | 41 | empty |
| 3 | 979 | 0.82 | 0.83 | 85 | empty |
| 4 | 317 | 0.79 | 0.90 | 73 | ATP, MG |
| 5 | 108 | 0.79 | 0.97 | 36 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1844 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1606 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 1169 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1032 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1013 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7O17 · ABC transporter NosDFY E154Q, ATP-bound in lipid nanodisc · the same entry in another collection · chain E against E, TM-score 1.00
- P19845 · AlphaFold monomer V2.0 prediction for probable ABC transporter permease protein nosy… · a predicted model of the same protein · chain D against A, TM-score 0.94
- P19843 · AlphaFold monomer V2.0 prediction for probable ABC transporter binding protein nosd… · a predicted model of the same protein · chain A against A, TM-score 0.91
- P19844 · AlphaFold monomer V2.0 prediction for probable ABC transporter ATP- binding protein nosf… · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P19843
- Every structure of UniProt P19844
- Every structure of UniProt P19845
- Elsewhere: RCSB PDB 7O17 · PDBe 7O17 · UniProt P19843 · UniProt P19844 · UniProt P19845
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