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Crystal structure of selenomethionine variant of bacillus anthracis immune inhibitor A2 peptidase zymogen
Analyse Crystal structure of selenomethionine variant of bacillus anthracis immune… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YU5
- Type
- protein
- Length
- 1,384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immune inhibitor a, metalloprotease
- EC
- 3.4.24.-
- UniProt
- D8H130
- Ligands
- KH2, CA, ZN, K
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immune inhibitor a, metalloprotease (EC 3.4.24.-) | protein | 695 | 19% helix, 30% strand | D8H130 |
| B | Immune inhibitor a, metalloprotease (EC 3.4.24.-) | protein | 689 | 18% helix, 30% strand | D8H130 |
Ligands and binding sites
- KH2 · 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate · ligand · 2 copies · chains A
- CA · Calcium ion · metal · 8 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains B
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.81 | 0.87 | 55 | empty |
| 2 | 508 | 0.81 | 0.88 | 51 | empty |
| 3 | 241 | 0.66 | 0.84 | 48 | empty |
| 4 | 187 | 0.63 | 0.84 | 34 | empty |
| 5 | 105 | 0.53 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 270 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4YU5 · Crystal structure of selenomethionine variant of Bacillus anthracis immune inhibitor A2… · 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 D8H130
- Elsewhere: RCSB PDB 4YU5 · PDBe 4YU5 · UniProt D8H130
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