MolNFT v1 · #124757 · protein
Crystal structure of the competence-damaged protein (cina) superfamily protein ECK1530/EC0983 from escherichia COLI
5KOL · Uncharacterized protein: “Crystal structure of the competence-damaged protein (cina) superfamily protein ECK1530/EC0983 from…”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.70). MolNFT v1 #124757 on GenesisL1: 3D…
- PDB
- 5KOL
- Type
- protein
- Length
- 691 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q8XB29
- Ligands
- CL
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Uncharacterized protein | protein | 173 | 42% helix, 20% strand | Q8XB29 |
| D | Uncharacterized protein | protein | 172 | 42% helix, 20% strand | Q8XB29 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.70 | 0.78 | 76 | empty |
| 2 | 91 | 0.60 | 0.88 | 20 | empty |
| 3 | 258 | 0.52 | 0.75 | 36 | empty |
| 4 | 283 | 0.52 | 0.74 | 44 | empty |
| 5 | 227 | 0.49 | 0.75 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–C · 955 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 892 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 251 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 215 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KOL · Crystal structure of the competence-damaged protein (CinA) superfamily protein… · 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 Q8XB29
- Elsewhere: RCSB PDB 5KOL · PDBe 5KOL · UniProt Q8XB29
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