MolNFT v1 · #183725 · protein
ABC transporter nosdfy, nucleotide-free in lipid nanodisc, R-domain 3
7O16 · Probable ABC transporter binding protein nosd: “ABC transporter nosdfy, nucleotide-free in lipid nanodisc, R-domain 3”. Electron microscopy, 1 ligand (MG), 10 pockets (best druggability 0.81). MolNFT v1 #183725 on GenesisL1: 3D…
- PDB
- 7O16
- 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 | 34% helix, 21% strand | P19844 |
| C | Probable ABC transporter ATP-binding protein nosf | protein | 298 | 31% helix, 20% strand | P19844 |
| D | Probable ABC transporter permease protein nosy | protein | 267 | 78% 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.81 | 0.83 | 115 | empty |
| 2 | 998 | 0.81 | 0.82 | 93 | empty |
| 3 | 350 | 0.73 | 0.85 | 42 | empty |
| 4 | 55 | 0.66 | 0.94 | 19 | empty |
| 5 | 89 | 0.60 | 0.87 | 17 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1443 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1159 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 1142 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 939 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 834 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7O16 · ABC transporter NosDFY, nucleotide-free in lipid nanodisc, R-domain 3 · 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 B 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 E 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 P19843
- Every structure of UniProt P19844
- Every structure of UniProt P19845
- Elsewhere: RCSB PDB 7O16 · PDBe 7O16 · UniProt P19843 · UniProt P19844 · UniProt P19845
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