Research workbench
Crystal structure of susd superfamily protein (YP_001297730.1) from bacteroides vulgatus atcc 8482 at 1.55 a resolution
Analyse Crystal structure of susd superfamily protein (YP_001297730.1) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JQ1
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Susd superfamily protein
- UniProt
- A6KXE4
- Ligands
- CA, CL
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Susd superfamily protein | protein | 462 | 52% helix, 7% strand | A6KXE4 |
| B | Susd superfamily protein | protein | 464 | 52% helix, 7% strand | A6KXE4 |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, B
- CL · Chloride ion · ion · 11 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.84 | 0.85 | 128 | CA, CL |
| 2 | 71 | 0.74 | 0.98 | 30 | empty |
| 3 | 77 | 0.62 | 0.90 | 23 | empty |
| 4 | 117 | 0.53 | 0.82 | 20 | EDO |
| 5 | 75 | 0.45 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 924 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3JQ1 · Crystal structure of SusD superfamily protein (YP_001297730.1) from Bacteroides vulgatus… · 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 A6KXE4
- Elsewhere: RCSB PDB 3JQ1 · PDBe 3JQ1 · UniProt A6KXE4
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