Research workbench
ABC transporter nosdfy, nucleotide-free in gdn
Analyse ABC transporter nosdfy, nucleotide-free in gdn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O0Y
- Type
- protein
- Length
- 1,514 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
- MG
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ABC transporter binding protein nosd | protein | 402 | 6% helix, 36% strand | P19843 |
| B | Probable ABC transporter ATP-binding protein nosf | protein | 299 | 35% helix, 21% strand | P19844 |
| C | Probable ABC transporter ATP-binding protein nosf | protein | 298 | 32% helix, 21% strand | P19844 |
| D | Probable ABC transporter permease protein nosy | protein | 267 | 76% helix, 0% strand | P19845 |
| E | Probable ABC transporter permease protein nosy | protein | 248 | 76% helix, 0% strand | P19845 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.81 | 0.81 | 102 | empty |
| 2 | 821 | 0.80 | 0.83 | 97 | empty |
| 3 | 356 | 0.72 | 0.84 | 41 | empty |
| 4 | 85 | 0.55 | 0.85 | 17 | empty |
| 5 | 168 | 0.51 | 0.79 | 25 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1626 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1168 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 1136 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1017 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 850 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7O0Y · ABC transporter NosDFY, nucleotide-free in GDN · the same entry in another collection · chain E against E, TM-score 1.00
- P19844 · AlphaFold monomer V2.0 prediction for probable ABC transporter ATP- binding protein nosf… · a predicted model of the same protein · chain C against A, TM-score 0.97
- 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 0.96
- 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
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 7O0Y · PDBe 7O0Y · UniProt P19843 · UniProt P19844 · UniProt P19845
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