Research workbench
Crystal structure of a susd superfamily protein (BF1802) from bacteroides fragilis nctc 9343 at 1.90 a resolution
Analyse Crystal structure of a susd superfamily protein (BF1802) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NQP
- Type
- protein
- Length
- 973 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Susd superfamily protein
- UniProt
- Q5LEF0
- Pockets
- 10 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Susd superfamily protein | protein | 486 | 46% helix, 9% strand | Q5LEF0 |
| B | Susd superfamily protein | protein | 487 | 48% helix, 9% strand | Q5LEF0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.54 | 0.73 | 51 | EDO |
| 2 | 60 | 0.46 | 0.84 | 15 | EDO |
| 3 | 67 | 0.44 | 0.81 | 15 | EDO |
| 4 | 85 | 0.35 | 0.75 | 15 | empty |
| 5 | 76 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 156 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3NQP · Crystal structure of a SusD superfamily protein (BF1802) 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 Q5LEF0
- Elsewhere: RCSB PDB 3NQP · PDBe 3NQP · UniProt Q5LEF0
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