MolNFT v1 · #183722 · protein
ABC transporter nosdfy, amppnp-bound in gdn
7O12 · Probable ABC transporter ATP-binding protein nosf: “ABC transporter nosdfy, amppnp-bound in gdn”. Electron microscopy, 2 ligands (ANP, MG), 11 pockets (best druggability 0.82). MolNFT v1 #183722 on GenesisL1: 3D structure, binding…
- PDB
- 7O12
- Type
- protein
- Length
- 1,511 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ABC transporter ATP-binding protein nosf; Probable ABC transporter binding…
- UniProt
- P19844, P19843, P19845
- Ligands
- ANP, MG
- Pockets
- 11 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Probable ABC transporter ATP-binding protein nosf | protein | 298 | 35% helix, 21% strand | P19844 |
| A | Probable ABC transporter binding protein nosd | protein | 402 | 7% helix, 37% strand | P19843 |
| E | Probable ABC transporter permease protein nosy | protein | 246 | 76% helix, 0% strand | P19845 |
| D | Probable ABC transporter permease protein nosy | protein | 267 | 78% helix, 0% strand | P19845 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 3 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.82 | 0.84 | 86 | empty |
| 2 | 1126 | 0.74 | 0.77 | 99 | empty |
| 3 | 292 | 0.72 | 0.85 | 33 | empty |
| 4 | 332 | 0.62 | 0.79 | 54 | MG, ANP |
| 5 | 61 | 0.55 | 0.88 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1618 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1121 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 1119 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 971 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 853 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7O12 · ABC transporter NosDFY, AMPPNP-bound in GDN · the same entry in another collection · chain D against D, TM-score 1.00
- 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
- 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 0.95
- 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 P19844
- Every structure of UniProt P19843
- Every structure of UniProt P19845
- Elsewhere: RCSB PDB 7O12 · PDBe 7O12 · UniProt P19844 · UniProt P19843 · UniProt P19845
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