MolNFT v1 · #66301 · protein
Mutant endolysin from bacillus subtilis
3HMB · N-acetylmuramoyl-L-alanine amidase xlya: “Mutant endolysin from bacillus subtilis”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.66). MolNFT v1 #66301 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HMB
- Type
- protein
- Length
- 464 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylmuramoyl-L-alanine amidase xlya
- EC
- 3.5.1.28
- UniProt
- P39800
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | N-acetylmuramoyl-L-alanine amidase xlya (EC 3.5.1.28) | protein | 154 | 31% helix, 17% strand | P39800 |
| B | N-acetylmuramoyl-L-alanine amidase xlya (EC 3.5.1.28) | protein | 156 | 31% helix, 17% strand | P39800 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.66 | 0.77 | 58 | empty |
| 2 | 72 | 0.30 | 0.74 | 19 | empty |
| 3 | 72 | 0.29 | 0.73 | 18 | empty |
| 4 | 52 | 0.27 | 0.74 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 537 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 4 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 P39800
- Elsewhere: RCSB PDB 3HMB · PDBe 3HMB · UniProt P39800
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.