Research workbench
2.05 ångström resolution crystal structure of epidermin leader peptide processing serine protease (epip) from staphylococcus aureus.
Analyse 2.05 ångström resolution crystal structure of epidermin leader peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QFH
- Type
- protein
- Length
- 3,395 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermin leader peptide processing serine protease epip
- EC
- 3.4.21.-
- UniProt
- Q5HEV5
- Ligands
- NA, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermin leader peptide processing serine protease epip (EC 3.4.21.-) | protein | 424 | 33% helix, 21% strand | Q5HEV5 |
| B | Epidermin leader peptide processing serine protease epip (EC 3.4.21.-) | protein | 425 | 33% helix, 20% strand | Q5HEV5 |
| C, G | Epidermin leader peptide processing serine protease epip (EC 3.4.21.-) | protein | 421 | 33% helix, 20% strand | Q5HEV5 |
| D, E, F, H | Epidermin leader peptide processing serine protease epip (EC 3.4.21.-) | protein | 426 | 34% helix, 20% strand | Q5HEV5 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, D, H
- SO4 · Sulfate ion · ion · 38 copies · chains A, F, H, B, E, C, G, D
- GOL · Glycerol · additive · 4 copies · chains A, D, B, E
- EDO · 1,2-ethanediol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.83 | 0.84 | 124 | GOL, SO4 |
| 2 | 879 | 0.82 | 0.84 | 102 | SO4 |
| 3 | 544 | 0.77 | 0.84 | 68 | empty |
| 4 | 910 | 0.72 | 0.76 | 84 | SO4 |
| 5 | 690 | 0.71 | 0.78 | 53 | SO4 |
Interfaces
13 interfaces between chains.
- B–D · 935 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 934 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 901 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 895 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3QFH · 2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine… · 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 Q5HEV5
- Elsewhere: RCSB PDB 3QFH · PDBe 3QFH · UniProt Q5HEV5
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