Research workbench
Hemoglobin protease (hbp) passenger missing domain-2
Analyse Hemoglobin protease (hbp) passenger missing domain-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AK5
- Type
- protein
- Length
- 3,840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-binding protease hbp
- EC
- 3.4.21.-
- UniProt
- O88093
- Ligands
- CA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemoglobin-binding protease hbp (EC 3.4.21.-) | protein | 970 | 7% helix, 46% strand | O88093 |
| C | Hemoglobin-binding protease hbp (EC 3.4.21.-) | protein | 952 | 7% helix, 46% strand | O88093 |
| D | Hemoglobin-binding protease hbp (EC 3.4.21.-) | protein | 948 | 7% helix, 46% strand | O88093 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.71 | 0.82 | 47 | empty |
| 2 | 433 | 0.71 | 0.82 | 44 | empty |
| 3 | 457 | 0.71 | 0.81 | 46 | empty |
| 4 | 689 | 0.70 | 0.78 | 73 | empty |
| 5 | 404 | 0.70 | 0.82 | 47 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1239 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 413 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3AK5 · Hemoglobin protease (Hbp) passenger missing domain-2 · the same entry in another collection · chain A against A, TM-score 1.00
- O88093 · AlphaFold monomer V2.0 prediction for hemoglobin-binding protease hbp autotransporter… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O88093
- Elsewhere: RCSB PDB 3AK5 · PDBe 3AK5 · UniProt O88093
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