MolNFT v1 · #109830 · protein
Crystal structure of putative M16-like peptidase from alicyclobacillus acidocaldarius
4XEA · Peptidase M16 domain protein: “Crystal structure of putative M16-like peptidase from alicyclobacillus acidocaldarius”. X-ray diffraction, 2 ligands (NA, NI), 6 pockets (best druggability 0.60). MolNFT v1 #109830 on GenesisL1: 3D…
- PDB
- 4XEA
- Type
- protein
- Length
- 423 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase M16 domain protein
- UniProt
- C8WVD6
- Ligands
- NA, NI
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase M16 domain protein | protein | 423 | 45% helix, 20% strand | C8WVD6 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.60 | 0.76 | 39 | empty |
| 2 | 145 | 0.44 | 0.76 | 29 | empty |
| 3 | 101 | 0.41 | 0.77 | 20 | ACT |
| 4 | 90 | 0.39 | 0.77 | 23 | empty |
| 5 | 50 | 0.38 | 0.81 | 15 | empty |
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4XEA · Crystal structure of putative M16-like peptidase from Alicyclobacillus acidocaldarius · 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 C8WVD6
- Elsewhere: RCSB PDB 4XEA · PDBe 4XEA · UniProt C8WVD6
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