MolNFT v1 · #31615 · protein
Truncated S. aureus lytm, P212121 crystal form
2B0P · Glycyl-glycine endopeptidase lytm: “Truncated S. aureus lytm, P212121 crystal form”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.53). MolNFT v1 #31615 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2B0P
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycyl-glycine endopeptidase lytm
- EC
- 3.4.24.75
- UniProt
- O33599
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycyl-glycine endopeptidase lytm (EC 3.4.24.75) | protein | 129 | 10% helix, 43% strand | O33599 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.53 | 0.77 | 47 | CAC |
| 2 | 84 | 0.33 | 0.74 | 24 | CAC |
| 3 | 58 | 0.29 | 0.75 | 18 | ACT |
Interfaces
1 interface between chains.
- A–B · 482 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 O33599
- Elsewhere: RCSB PDB 2B0P · PDBe 2B0P · UniProt O33599
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