Research workbench
Helicobacter pylori adhesin hopq type I bound to the N-terminal domain of human CEACAM1
Analyse Helicobacter pylori adhesin hopq type I bound to the N-terminal domain of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GBG
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carcinoembryonic antigen-related cell adhesion molecule 1; Outer membrane protein
- UniProt
- P13688, B5Z8H1
- Ligands
- BR
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Carcinoembryonic antigen-related cell adhesion molecule 1 | protein | 110 | 8% helix, 54% strand | P13688 |
| A | Outer membrane protein | protein | 321 | 58% helix, 13% strand | B5Z8H1 |
Ligands and binding sites
- BR · Bromide ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.45 | 0.77 | 18 | empty |
| 2 | 136 | 0.40 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- D–A · 1057 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6GBG · Helicobacter pylori adhesin HopQ type I bound to the N-terminal domain of human CEACAM1 · the same entry in another collection · chain D against D, TM-score 1.00
- P13688 · AlphaFold monomer V2.0 prediction for carcinoembryonic antigen- related cell adhesion… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P13688
- Every structure of UniProt B5Z8H1
- Elsewhere: RCSB PDB 6GBG · PDBe 6GBG · UniProt P13688 · UniProt B5Z8H1
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