MolNFT v1 · #95896 · protein
The crystal structure of a secreted protein esxb (mutant P67A) from bacillus anthracis str. sterne
4J41: “The crystal structure of a secreted protein esxb (mutant P67A) from bacillus anthracis str. sterne”. X-ray diffraction, 4 pockets (best druggability 0.58). MolNFT v1 #95896 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4J41
- Type
- protein
- Length
- 501 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted protein esxb
- UniProt
- Q81R67
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secreted protein esxb | protein | 89 | 81% helix, 0% strand | Q81R67 |
| B | Secreted protein esxb | protein | 86 | 83% helix, 0% strand | Q81R67 |
| C, E | Secreted protein esxb | protein | 81 | 89% helix, 0% strand | Q81R67 |
| D | Secreted protein esxb | protein | 84 | 87% helix, 0% strand | Q81R67 |
| F | Secreted protein esxb | protein | 80 | 90% helix, 0% strand | Q81R67 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D, E, F
- FMT · Formic acid · additive · 2 copies · chains C, D
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.58 | 0.76 | 36 | empty |
| 2 | 157 | 0.53 | 0.80 | 33 | PEG |
| 3 | 214 | 0.47 | 0.74 | 32 | empty |
| 4 | 50 | 0.32 | 0.77 | 14 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1652 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1558 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 339 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4J41 · The crystal structure of a secreted protein EsxB (Mutant P67A) from Bacillus anthracis… · 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 Q81R67
- Elsewhere: RCSB PDB 4J41 · PDBe 4J41 · UniProt Q81R67
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