Research workbench
Crystal structure of putative binding component of ABC transporter from wolinella succinogenes dsm 1740 complexed with lysine
Analyse Crystal structure of putative binding component of ABC transporter from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K4U
- Type
- protein
- Length
- 1,399 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Binding component of ABC transporter
- UniProt
- Q7MAG0
- Ligands
- LYS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Binding component of ABC transporter | protein | 233 | 39% helix, 24% strand | Q7MAG0 |
| E | Binding component of ABC transporter | protein | 234 | 39% helix, 24% strand | Q7MAG0 |
Ligands and binding sites
- LYS · Lysine · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.82 | 0.83 | 94 | empty |
| 2 | 464 | 0.73 | 0.82 | 45 | empty |
| 3 | 319 | 0.58 | 0.77 | 39 | empty |
| 4 | 283 | 0.54 | 0.76 | 38 | empty |
| 5 | 272 | 0.54 | 0.76 | 35 | empty |
Interfaces
9 interfaces between chains.
- D–F · 624 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 609 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 608 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 606 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 605 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3K4U · CRYSTAL STRUCTURE OF putative binding component of ABC transporter from Wolinella… · the same entry in another collection · chain A against A, 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 Q7MAG0
- Elsewhere: RCSB PDB 3K4U · PDBe 3K4U · UniProt Q7MAG0
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