Research workbench
Crystal structure of a leucine-rich repeat protein (EUBVEN_01088) from eubacterium ventriosum atcc 27560 at 2.50 a resolution
Analyse Crystal structure of a leucine-rich repeat protein (EUBVEN_01088) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H09
- Type
- protein
- Length
- 1,869 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical leucine rich repeat protein
- UniProt
- A5Z5V6
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical leucine rich repeat protein | protein | 374 | 2% helix, 28% strand | A5Z5V6 |
| B | Hypothetical leucine rich repeat protein | protein | 372 | 2% helix, 27% strand | A5Z5V6 |
| C | Hypothetical leucine rich repeat protein | protein | 373 | 2% helix, 28% strand | A5Z5V6 |
| D | Hypothetical leucine rich repeat protein | protein | 377 | 2% helix, 27% strand | A5Z5V6 |
| E | Hypothetical leucine rich repeat protein | protein | 373 | 2% helix, 28% strand | A5Z5V6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 38 copies · chains A, B, E, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.76 | 0.79 | 114 | PEG, EDO |
| 2 | 296 | 0.59 | 0.78 | 44 | EDO |
| 3 | 312 | 0.58 | 0.77 | 41 | EDO |
| 4 | 193 | 0.55 | 0.79 | 24 | EDO |
| 5 | 301 | 0.49 | 0.73 | 36 | empty |
Interfaces
7 interfaces between chains.
- A–B · 888 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 419 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 215 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 151 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 4H09 · Crystal structure of a leucine-rich repeat protein (EUBVEN_01088) from Eubacterium… · 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 A5Z5V6
- Elsewhere: RCSB PDB 4H09 · PDBe 4H09 · UniProt A5Z5V6
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