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The crystal structure of a secreted protein esxb (semet-labeled, C- term. his-tagged) from bacillus anthracis str. sterne
Analyse The crystal structure of a secreted protein esxb (semet-labeled, C- term.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IYH
- Type
- protein
- Length
- 322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted protein esxb
- UniProt
- Q81R67
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secreted protein esxb | protein | 81 | 89% helix, 0% strand | Q81R67 |
| B, D | Secreted protein esxb | protein | 80 | 80% helix, 0% strand | Q81R67 |
| C | Secreted protein esxb | protein | 81 | 90% helix, 0% strand | Q81R67 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, D, C
- FMT · Formic acid · additive · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.41 | 0.75 | 21 | empty |
| 2 | 111 | 0.40 | 0.75 | 19 | SO4 |
| 3 | 74 | 0.35 | 0.76 | 16 | EDO, SO4 |
| 4 | 69 | 0.32 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3175 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 3149 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 442 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4IYH · The crystal structure of a secreted protein EsxB (SeMet-labeled, C-term. His-Tagged) from… · 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 4IYH · PDBe 4IYH · UniProt Q81R67
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