MolNFT v2 · #212648 · protein
Crystal structure of Bacillus subtilis LytE in complex with IseA
8I2E · Uncharacterized protein YoeB: “Crystal structure of Bacillus subtilis LytE in complex with IseA”. X-ray diffraction at 3.2, 5 pockets (best druggability 0.64). MolNFT v2 #212648 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 8I2E
- Type
- protein
- Length
- 542 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Bacillus subtilis subsp. subtilis str. 168
- Molecule
- Uncharacterized protein YoeB; Probable peptidoglycan endopeptidase LytE
- EC
- 3.4.-.-
- UniProt
- O34841, P54421
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · resolution 3.2 · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein YoeB | protein | 153 | 27% helix, 33% strand | O34841 |
| B, D | Probable peptidoglycan endopeptidase LytE (EC 3.4.-.-) | protein | 118 | 25% helix, 31% strand | P54421 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.64 | 0.75 | 60 | empty |
| 2 | 80 | 0.43 | 0.80 | 16 | empty |
| 3 | 112 | 0.39 | 0.75 | 23 | empty |
| 4 | 83 | 0.35 | 0.76 | 19 | empty |
| 5 | 70 | 0.31 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1154 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1131 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 557 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- P54421 · AlphaFold monomer V2.0 prediction for probable peptidoglycan endopeptidase lyte (P54421) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O34841
- Every structure of UniProt P54421
- Elsewhere: RCSB PDB 8I2E · PDBe 8I2E · UniProt O34841 · UniProt P54421
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