MolNFT v1 · #179051 · protein
Structure of impa from pseudomonas aeruginosa in complex with an O- glycopeptide
7JTV · Immunomodulating metalloprotease: “Structure of impa from pseudomonas aeruginosa in complex with an O- glycopeptide”. X-ray diffraction, 3 ligands (A2G, GAL, ZN), 17 pockets (best druggability 0.64). MolNFT v1 #179051 on GenesisL1…
- PDB
- 7JTV
- Type
- protein
- Length
- 1,776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunomodulating metalloprotease; Glu-ala-pro-ser-ala
- EC
- 3.4.24.-
- UniProt
- Q9I5W4
- Ligands
- A2G, GAL, ZN
- Pockets
- 17 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Immunomodulating metalloprotease (EC 3.4.24.-) | protein | 883 | 40% helix, 15% strand | Q9I5W4 |
| A | Immunomodulating metalloprotease (EC 3.4.24.-) | protein | 884 | 39% helix, 15% strand | Q9I5W4 |
| E | Glu-ala-pro-ser-ala | protein | 5 | 0% helix, 0% strand | — |
| H | Glu-ala-pro-ser-ala | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains B, E, A, H
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 10 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.64 | 0.77 | 56 | empty |
| 2 | 369 | 0.62 | 0.78 | 41 | empty |
| 3 | 349 | 0.61 | 0.78 | 41 | empty |
| 4 | 330 | 0.60 | 0.77 | 56 | empty |
| 5 | 188 | 0.54 | 0.79 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1066 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 220 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 203 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
- 7JTV · Structure of IMPa from Pseudomonas aeruginosa in complex with an O-glycopeptide · the same entry in another collection · chain B against B, TM-score 1.00
- Q9I5W4 · AlphaFold monomer V2.0 prediction for immunomodulating metalloprotease (Q9I5W4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9I5W4
- Elsewhere: RCSB PDB 7JTV · PDBe 7JTV · UniProt Q9I5W4
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