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Crystal structure of putative cell invasion protein with MAC/PERFORIN domain (NP_812351.1) from bacteriodes thetaiotaomicron vpi-5482 at 2.46 a resolution
Analyse Crystal structure of putative cell invasion protein with MAC/PERFORIN domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KK7
- Type
- protein
- Length
- 1,001 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cell invasion protein with MAC/PERFORIN domain
- UniProt
- Q8A267
- Ligands
- CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative cell invasion protein with MAC/PERFORIN domain | protein | 502 | 31% helix, 32% strand | Q8A267 |
| B | Putative cell invasion protein with MAC/PERFORIN domain | protein | 499 | 31% helix, 31% strand | Q8A267 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.78 | 0.80 | 117 | MPD |
| 2 | 99 | 0.53 | 0.83 | 26 | empty |
| 3 | 107 | 0.49 | 0.81 | 22 | empty |
| 4 | 105 | 0.49 | 0.81 | 22 | empty |
| 5 | 83 | 0.37 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 728 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3KK7 · Crystal structure of Putative cell invasion protein with MAC/Perforin domain… · 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 Q8A267
- Elsewhere: RCSB PDB 3KK7 · PDBe 3KK7 · UniProt Q8A267
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