Research workbench
Crystal structure of a DUF4784 family protein (BACCAC_01631) from bacteroides caccae atcc 43185 at 2.50 a resolution
Analyse Crystal structure of a DUF4784 family protein (BACCAC_01631) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M8R
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- A5ZFG7
- Ligands
- PO4, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein | protein | 406 | 1% helix, 49% strand | A5ZFG7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 11 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.76 | 0.95 | 36 | EDO |
| 2 | 733 | 0.75 | 0.80 | 66 | PO4, EDO |
| 3 | 221 | 0.70 | 0.87 | 48 | EDO |
| 4 | 568 | 0.69 | 0.78 | 52 | empty |
| 5 | 449 | 0.66 | 0.79 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4M8R · Crystal structure of a DUF4784 family protein (BACCAC_01631) from Bacteroides caccae 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 A5ZFG7
- Elsewhere: RCSB PDB 4M8R · PDBe 4M8R · UniProt A5ZFG7
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