MolNFT v1 · #76270 · protein
2.05 ångström resolution crystal structure of epidermin leader peptide processing serine protease (epip) from staphylococcus aureus.
3QFH · Epidermin leader peptide processing serine protease epip: “2.05 ångström resolution crystal structure of epidermin leader peptide processing serine protease (epip) from…”. X-ray diffraction, 2 ligands (NA, SO4), 20 pockets (best…
- 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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