Research workbench
Crystal structure of a putative secreted protein (BF4250) from bacteroides fragilis nctc 9343 at 1.81 a resolution
Analyse Crystal structure of a putative secreted protein (BF4250) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OWR
- Type
- protein
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized hypothetical protein
- UniProt
- Q5L7M9
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized hypothetical protein | protein | 127 | 8% helix, 53% strand | Q5L7M9 |
| B, C | Uncharacterized hypothetical protein | protein | 128 | 8% helix, 52% strand | Q5L7M9 |
| D | Uncharacterized hypothetical protein | protein | 129 | 6% helix, 52% strand | Q5L7M9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.61 | 0.90 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 341 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 335 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 286 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3OWR · Crystal structure of a putative secreted protein (BF4250) from Bacteroides fragilis NCTC… · 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 Q5L7M9
- Elsewhere: RCSB PDB 3OWR · PDBe 3OWR · UniProt Q5L7M9
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