MolNFT v1 · #167120 · protein
2.60 ångström resolution crystal structure of peptidase S41 from acinetobacter baumannii
6VBB: “2.60 ångström resolution crystal structure of peptidase S41 from acinetobacter baumannii”. X-ray diffraction, 3 ligands (TMO, NA, CL), 5 pockets (best druggability 0.69). MolNFT v1 #167120 on GenesisL1: 3D structure, binding sites…
- PDB
- 6VBB
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase S41
- UniProt
- A0A1E3M7A1
- Ligands
- TMO, NA, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase S41 | protein | 345 | 28% helix, 26% strand | A0A1E3M7A1 |
| B | Peptidase S41 | protein | 341 | 28% helix, 27% strand | A0A1E3M7A1 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.69 | 0.80 | 46 | empty |
| 2 | 448 | 0.65 | 0.78 | 50 | empty |
| 3 | 199 | 0.59 | 0.81 | 35 | empty |
| 4 | 241 | 0.58 | 0.79 | 37 | empty |
| 5 | 57 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2257 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 6VBB · 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 from Acinetobacter baumannii · 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 A0A1E3M7A1
- Elsewhere: RCSB PDB 6VBB · PDBe 6VBB · UniProt A0A1E3M7A1
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