MolNFT v1 · #68730 · protein
Crystal structure of putative binding component of ABC transporter from wolinella succinogenes dsm 1740 complexed with lysine
3K4U: “Crystal structure of putative binding component of ABC transporter from wolinella succinogenes dsm 1740…”. X-ray diffraction, 1 ligand (LYS), 20 pockets (best druggability 0.82). MolNFT v1 #68730 on GenesisL1: 3D structure, binding…
- 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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