Research workbench
Crystal structure of a DUF4425 family protein (BACOVA_05332) from bacteroides ovatus atcc 8483 at 2.52 a resolution
Analyse Crystal structure of a DUF4425 family protein (BACOVA_05332) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QEY
- Type
- protein
- Length
- 1,243 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A7M5D7
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, H, I | Uncharacterized protein | protein | 125 | 2% helix, 62% strand | A7M5D7 |
| B, C, E, F, J | Uncharacterized protein | protein | 124 | 2% helix, 62% strand | A7M5D7 |
| D | Uncharacterized protein | protein | 123 | 2% helix, 63% strand | A7M5D7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, F, E, B, C, D, J, G, H
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, E, B, C, D, I, J
- PGE · Triethylene glycol · additive · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.69 | 0.77 | 81 | empty |
| 2 | 517 | 0.68 | 0.79 | 76 | EDO |
| 3 | 503 | 0.68 | 0.79 | 72 | EDO, PEG |
| 4 | 480 | 0.68 | 0.79 | 63 | EDO |
| 5 | 448 | 0.67 | 0.79 | 64 | EDO |
Interfaces
20 interfaces between chains.
- F–G · 676 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 664 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 663 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 650 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 647 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4QEY · Crystal structure of a DUF4425 family protein (BACOVA_05332) from Bacteroides ovatus ATCC… · 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 A7M5D7
- Elsewhere: RCSB PDB 4QEY · PDBe 4QEY · UniProt A7M5D7
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