MolNFT v1 · #111302 · protein
Crystal structure of an amino acid ABC transporter with atps
4YMV · ABC-type polar amino acid transport system, ATPase component: “Crystal structure of an amino acid ABC transporter with atps”. X-ray diffraction, 1 ligand (ATP), 11 pockets (best druggability 0.71). MolNFT v1 #111302 on GenesisL1: 3D…
- PDB
- 4YMV
- Type
- protein
- Length
- 909 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type polar amino acid transport system, ATPase component; ABC-type amino acid…
- UniProt
- Q8RCC2, Q8RCC3
- Ligands
- ATP
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, A | ABC-type polar amino acid transport system, ATPase component | protein | 240 | 39% helix, 25% strand | Q8RCC2 |
| D | ABC-type amino acid transport system, permease component | protein | 215 | 81% helix, 0% strand | Q8RCC3 |
| C | ABC-type amino acid transport system, permease component | protein | 214 | 80% helix, 0% strand | Q8RCC3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains J, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.71 | 0.79 | 56 | empty |
| 2 | 656 | 0.67 | 0.76 | 58 | ATP |
| 3 | 90 | 0.37 | 0.75 | 16 | empty |
| 4 | 87 | 0.36 | 0.75 | 16 | empty |
| 5 | 71 | 0.34 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- D–C · 1627 Ų buried · 16 hydrogen bonds · protein-protein
- J–C · 872 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 862 Ų buried · 11 hydrogen bonds · protein-protein
- J–A · 602 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4YMV · Crystal structure of an amino acid ABC transporter with ATPs · the same entry in another collection · chain J against J, TM-score 1.00
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 Q8RCC2
- Every structure of UniProt Q8RCC3
- Elsewhere: RCSB PDB 4YMV · PDBe 4YMV · UniProt Q8RCC2 · UniProt Q8RCC3
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