Research workbench
Crystal structure of mamo protease domain from magnetospirillum magneticum (ni bound form)
Analyse Crystal structure of mamo protease domain from magnetospirillum magneticum (ni… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HMA
- Type
- protein
- Length
- 196 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin-like serine protease; Unidentified peptide
- UniProt
- Q2W8Q2
- Ligands
- NI, CL
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trypsin-like serine protease | protein | 191 | 12% helix, 48% strand | Q2W8Q2 |
| C | Unidentified peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.38 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 328 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5HMA · Crystal structure of MamO protease domain from Magnetospirillum magneticum (Ni bound form) · the same entry in another collection · chain A against A, TM-score 1.00
- Q2W8Q2 · AlphaFold monomer V2.0 prediction for probable membrane transporter protein mamo (Q2W8Q2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q2W8Q2
- Elsewhere: RCSB PDB 5HMA · PDBe 5HMA · UniProt Q2W8Q2
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