MolNFT v1 · #31462 · protein
Crystal structure of monoclinic form of streptococcus mac-1
2AVW · IgG-degrading protease: “Crystal structure of monoclinic form of streptococcus mac-1”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.75). MolNFT v1 #31462 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2AVW
- Type
- protein
- Length
- 1,749 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG-degrading protease
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IgG-degrading protease | protein | 290 | 27% helix, 23% strand | — |
| B, C, F | IgG-degrading protease | protein | 289 | 26% helix, 23% strand | — |
| D, E | IgG-degrading protease | protein | 296 | 24% helix, 22% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.75 | 0.82 | 41 | empty |
| 2 | 567 | 0.74 | 0.82 | 46 | empty |
| 3 | 658 | 0.73 | 0.80 | 48 | empty |
| 4 | 191 | 0.60 | 0.82 | 32 | empty |
| 5 | 103 | 0.57 | 0.85 | 28 | SO4 |
Interfaces
7 interfaces between chains.
- A–B · 874 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 826 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 821 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 575 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 508 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2AVW · Crystal structure of monoclinic form of streptococcus Mac-1 · 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 2AVW · PDBe 2AVW
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.