MolNFT v1 · #149819 · protein
Helicobacter pylori adhesin hopq type II bound to the N-terminal domain of human CEACAM1
6GBH · Carcinoembryonic antigen-related cell adhesion molecule 1: “Helicobacter pylori adhesin hopq type II bound to the N-terminal domain of human CEACAM1”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 6GBH
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carcinoembryonic antigen-related cell adhesion molecule 1; Hopq
- UniProt
- P13688, Q8GDI6
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Carcinoembryonic antigen-related cell adhesion molecule 1 | protein | 108 | 8% helix, 54% strand | P13688 |
| C | Hopq | protein | 318 | 53% helix, 11% strand | Q8GDI6 |
| A | Hopq | protein | 318 | 55% helix, 11% strand | Q8GDI6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains B, D, C, A
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 | 555 | 0.68 | 0.78 | 65 | empty |
| 2 | 193 | 0.52 | 0.78 | 28 | empty |
| 3 | 152 | 0.45 | 0.76 | 32 | SO4 |
| 4 | 80 | 0.33 | 0.74 | 21 | SO4 |
| 5 | 78 | 0.33 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- D–C · 973 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 952 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 480 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6GBH · Helicobacter pylori adhesin HopQ type II bound to the N-terminal domain of human CEACAM1 · the same entry in another collection · chain B against B, 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 Q8GDI6
- Elsewhere: RCSB PDB 6GBH · PDBe 6GBH · UniProt P13688 · UniProt Q8GDI6
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