Research workbench
Crystal structure of pseudomonas aerginosa alkaline protease complexed with substance P(1-6)
Analyse Crystal structure of pseudomonas aerginosa alkaline protease complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VI1
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline metalloproteinase; Substance P1-6, rpkpqq
- EC
- 3.4.24.-
- UniProt
- Q03023
- Ligands
- CA, ZN
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline metalloproteinase (EC 3.4.24.-) | protein | 466 | 19% helix, 21% strand | Q03023 |
| B | Alkaline metalloproteinase (EC 3.4.24.-) | protein | 470 | 19% helix, 24% strand | Q03023 |
| C, D | Substance P1-6, rpkpqq | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.60 | 0.79 | 52 | empty |
| 2 | 381 | 0.59 | 0.76 | 46 | empty |
| 3 | 257 | 0.58 | 0.79 | 44 | empty |
| 4 | 164 | 0.40 | 0.73 | 33 | empty |
| 5 | 66 | 0.35 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 980 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 669 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3VI1 · Crystal structure of Pseudomonas aerginosa alkaline protease complexed with Substance… · the same entry in another collection · chain B against B, TM-score 1.00
- Q03023 · AlphaFold monomer V2.0 prediction for serralysin (Q03023) · 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 Q03023
- Elsewhere: RCSB PDB 3VI1 · PDBe 3VI1 · UniProt Q03023
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