Research workbench
Crystal structure of a M20 family metallo peptidase from streptococcus pneumoniae
Analyse Crystal structure of a M20 family metallo peptidase from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2POK
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase, M20/M25/M40 family
- UniProt
- Q97T10
- Ligands
- BGC, MN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase, M20/M25/M40 family | protein | 458 | 36% helix, 22% strand | Q97T10 |
| B | Peptidase, M20/M25/M40 family | protein | 456 | 35% helix, 22% strand | Q97T10 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.76 | 0.79 | 77 | empty |
| 2 | 810 | 0.71 | 0.77 | 64 | empty |
| 3 | 90 | 0.47 | 0.81 | 19 | empty |
| 4 | 85 | 0.45 | 0.81 | 18 | empty |
| 5 | 91 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3088 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 2POK · Crystal structure of a M20 family metallo peptidase from Streptococcus pneumoniae · 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 Q97T10
- Elsewhere: RCSB PDB 2POK · PDBe 2POK · UniProt Q97T10
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.