Research workbench
Structure of P. magnus protein L mutant bound to a mouse Fab
Analyse Structure of P. magnus protein L mutant bound to a mouse Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MHH
- Type
- protein
- Length
- 992 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab, light chain; Fab, heavy chain; Protein L domain C
- Ligands
- AEA
- Pockets
- 14 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab, light chain | protein | 219 | 5% helix, 53% strand | — |
| B | Fab, heavy chain | protein | 215 | 8% helix, 51% strand | — |
| D | Fab, heavy chain | protein | 214 | 10% helix, 53% strand | — |
| E | Protein L domain C | protein | 63 | 35% helix, 44% strand | — |
| F | Protein L domain C | protein | 62 | 31% helix, 45% strand | — |
Ligands and binding sites
- AEA · (2-amino-2-carbamoyl-ethylsulfanyl)-acetic acid · ligand · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.62 | 0.75 | 75 | empty |
| 2 | 503 | 0.60 | 0.74 | 56 | empty |
| 3 | 202 | 0.57 | 0.80 | 27 | empty |
| 4 | 129 | 0.45 | 0.78 | 22 | empty |
| 5 | 136 | 0.43 | 0.76 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1752 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1720 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 607 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 597 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1MHH · Structure of P. magnus protein L mutant bound to a mouse Fab · 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
- Elsewhere: RCSB PDB 1MHH · PDBe 1MHH
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.