MolNFT v1 · #184507 · protein
ABC transporter complex nosdfyl, R-domain 2
7OSH · Probable ABC transporter binding protein nosd: “ABC transporter complex nosdfyl, R-domain 2”. Electron microscopy, 3 ligands (MG, CU, ZN), 12 pockets (best druggability 0.80). MolNFT v1 #184507 on GenesisL1: 3D structure, binding…
- PDB
- 7OSH
- Type
- protein
- Length
- 1,665 residues
- Chains
- 6
- 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, Q52529
- Ligands
- MG, CU, ZN
- Pockets
- 12 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ABC transporter binding protein nosd | protein | 392 | 7% helix, 37% strand | P19843 |
| B | Probable ABC transporter ATP-binding protein nosf | protein | 308 | 30% helix, 22% strand | P19844 |
| C | Probable ABC transporter ATP-binding protein nosf | protein | 307 | 30% helix, 18% 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 | 75% helix, 0% strand | P19845 |
| H | Copper-binding lipoprotein nosl | protein | 143 | 22% helix, 13% strand | Q52529 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CU · Copper (II) ion · metal · chains A, H
- ZN · Zinc ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.80 | 0.82 | 105 | empty |
| 2 | 429 | 0.75 | 0.84 | 44 | empty |
| 3 | 269 | 0.72 | 0.86 | 33 | empty |
| 4 | 61 | 0.70 | 0.95 | 18 | empty |
| 5 | 699 | 0.65 | 0.74 | 84 | empty |
Interfaces
9 interfaces between chains.
- B–C · 2709 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1159 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 1139 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1128 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 925 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7OSH · ABC Transporter complex NosDFYL, R-domain 2 · the same entry in another collection · chain H against H, 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
- Q52529 · AlphaFold monomer V2.0 prediction for copper-binding lipoprotein nosl (Q52529) · a predicted model of the same protein · chain H 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
- 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 0.88
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
- Every structure of UniProt Q52529
- Elsewhere: RCSB PDB 7OSH · PDBe 7OSH · UniProt P19843 · UniProt P19844 · UniProt P19845 · UniProt Q52529
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