MolNFT v1 · #186822 · protein
Cryo-EM structure of nanodisc reconstituted ABCD1 in nucleotide bound outward open conformation
7RR9 · ATP-binding cassette sub-family D member 1: “Cryo-EM structure of nanodisc reconstituted ABCD1 in nucleotide bound outward open conformation”. Electron microscopy, 4 ligands (UNL, CLR, AGS), 20 pockets (best druggability 0.85).…
- PDB
- 7RR9
- Type
- protein
- Length
- 1,120 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-binding cassette sub-family D member 1
- EC
- 7.6.2.4
- UniProt
- P33897
- Ligands
- UNL, CLR, AGS, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-binding cassette sub-family D member 1 (EC 7.6.2.4) | protein | 560 | 64% helix, 9% strand | P33897 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.85 | 0.87 | 96 | MG, AGS |
| 2 | 955 | 0.78 | 0.80 | 93 | empty |
| 3 | 51 | 0.69 | 0.96 | 15 | empty |
| 4 | 82 | 0.61 | 0.89 | 23 | empty |
| 5 | 262 | 0.59 | 0.79 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 5785 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7RR9 · Cryo-EM Structure of Nanodisc reconstituted ABCD1 in nucleotide bound outward open… · the same entry in another collection · chain A against A, TM-score 1.00
- P33897 · AlphaFold monomer V2.0 prediction for ATP-binding cassette sub-family D member 1 (P33897) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P33897
- Elsewhere: RCSB PDB 7RR9 · PDBe 7RR9 · UniProt P33897
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