Research workbench
2.2A resolution structure of holo hemophore hasa from yersinia pestis
Analyse 2.2A resolution structure of holo hemophore hasa from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JET
- Type
- protein
- Length
- 1,789 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemophore hasa
- UniProt
- Q7CL15
- Ligands
- HEM, CL
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I, J | Hemophore hasa | protein | 179 | 26% helix, 37% strand | Q7CL15 |
| H | Hemophore hasa | protein | 178 | 24% helix, 36% strand | Q7CL15 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 10 copies · chains A, B, F, C, D, E, G, J, H, I
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.69 | 0.80 | 45 | HEM, CL |
| 2 | 481 | 0.69 | 0.79 | 52 | HEM, CL |
| 3 | 643 | 0.68 | 0.77 | 71 | empty |
| 4 | 669 | 0.63 | 0.74 | 78 | empty |
| 5 | 129 | 0.55 | 0.82 | 20 | HEM, CL |
Interfaces
13 interfaces between chains.
- D–I · 578 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 573 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 569 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 313 Ų buried · 3 hydrogen bonds · protein-protein
- A–I · 277 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JET · 2.2A resolution structure of Holo hemophore HasA from Yersinia pestis · 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 Q7CL15
- Elsewhere: RCSB PDB 4JET · PDBe 4JET · UniProt Q7CL15
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