Research workbench
Crystal structure of bacillus halodurans metallo peptidase
Analyse Crystal structure of bacillus halodurans metallo peptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HDI
- Type
- protein
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processing protease; Synthetic peptide
- UniProt
- Q9KA85
- Ligands
- CO, SO4
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Processing protease | protein | 414 | 47% helix, 19% strand | Q9KA85 |
| C | Synthetic peptide | protein | 14 | 0% helix, 0% strand | — |
| D | Synthetic peptide | protein | 17 | 0% helix, 6% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.84 | 0.84 | 129 | empty |
| 2 | 807 | 0.79 | 0.82 | 70 | empty |
| 3 | 145 | 0.59 | 0.84 | 27 | empty |
| 4 | 109 | 0.45 | 0.79 | 20 | empty |
| 5 | 123 | 0.43 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2930 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 726 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 165 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3HDI · Crystal structure of Bacillus halodurans metallo peptidase · 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 Q9KA85
- Elsewhere: RCSB PDB 3HDI · PDBe 3HDI · UniProt Q9KA85
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