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Crystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate from Deinococcus radiodurans
Analyse Crystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IFG
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 /…
- Molecule
- Zinc metalloprotease; Tripeptides (TYR-SER-ALA)
- UniProt
- Q9RVZ5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.45
Structure
x-ray diffraction · resolution 1.9 · 3 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc metalloprotease | protein | 430 | 29% helix, 34% strand | Q9RVZ5 |
| B | Zinc metalloprotease | protein | 432 | 29% helix, 34% strand | Q9RVZ5 |
| E, F | Tripeptides (TYR-SER-ALA) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, E, B, F
- FMT · Formic acid · additive · 13 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.45 | 0.79 | 29 | FMT |
| 2 | 130 | 0.43 | 0.76 | 20 | empty |
| 3 | 116 | 0.40 | 0.75 | 30 | FMT |
| 4 | 66 | 0.38 | 0.79 | 15 | empty |
| 5 | 107 | 0.37 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 488 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 382 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 376 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6IFG · Crystal structure of M1 zinc metallopeptidase E323A mutant bound to tyr-ser-ala substrate… · 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 Q9RVZ5
- Elsewhere: RCSB PDB 6IFG · PDBe 6IFG · UniProt Q9RVZ5
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