Research workbench
Crystal structure of an amino acid ABC transporter complex with arginines
Analyse Crystal structure of an amino acid ABC transporter complex with arginines in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YMT
- Type
- protein
- Length
- 910 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
- ARG
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, A | ABC-type polar amino acid transport system, ATPase component | protein | 240 | 42% helix, 25% strand | Q8RCC2 |
| C, B | ABC-type amino acid transport system, permease component | protein | 215 | 79% helix, 0% strand | Q8RCC3 |
Ligands and binding sites
- ARG · Arginine · ligand · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.71 | 0.80 | 56 | ARG |
| 2 | 671 | 0.68 | 0.77 | 65 | empty |
| 3 | 94 | 0.35 | 0.73 | 14 | empty |
| 4 | 75 | 0.34 | 0.75 | 14 | empty |
| 5 | 85 | 0.33 | 0.73 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–B · 1643 Ų buried · 17 hydrogen bonds · protein-protein
- J–C · 857 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 856 Ų buried · 11 hydrogen bonds · protein-protein
- J–A · 587 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4YMT · Crystal structure of an amino acid ABC transporter complex with arginines · 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 4YMT · PDBe 4YMT · UniProt Q8RCC2 · UniProt Q8RCC3
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