Research workbench
Streptococcus gordonii C123 DOMAIN(S)-structural and functional analysis
Analyse Streptococcus gordonii C123 DOMAIN(S)-structural and functional analysis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L0O
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin receptor
- UniProt
- P16952
- Ligands
- CA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agglutinin receptor | protein | 479 | 12% helix, 41% strand | P16952 |
| B | Agglutinin receptor | protein | 476 | 11% helix, 42% strand | P16952 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.69 | 0.77 | 78 | empty |
| 2 | 188 | 0.56 | 0.80 | 32 | empty |
| 3 | 68 | 0.49 | 0.84 | 21 | empty |
| 4 | 140 | 0.48 | 0.78 | 30 | empty |
| 5 | 88 | 0.38 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1102 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 7L0O · Streptococcus gordonii C123 Domain(s)-Structural and Functional Analysis · the same entry in another collection · chain A against A, TM-score 1.00
- P16952 · AlphaFold monomer V2.0 prediction for agglutinin receptor (P16952) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P16952
- Elsewhere: RCSB PDB 7L0O · PDBe 7L0O · UniProt P16952
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