MolNFT v1 · #162168 · protein
The extracellular domain of G6B-B in complex with Fab fragment and DP12 heparin oligosaccharide.
6R0X · Antibody Fab fragment heavy chain: “The extracellular domain of G6B-B in complex with Fab fragment and DP12 heparin oligosaccharide.”. X-ray diffraction, 5 ligands (SGN, IDS, A2G), 12 pockets (best druggability 0.65). MolNFT v1…
- PDB
- 6R0X
- Type
- protein
- Length
- 1,047 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment heavy chain; Antibody Fab fragment light chain; Megakaryocyte and…
- UniProt
- O95866
- Ligands
- SGN, IDS, A2G, GAL, SIA
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment heavy chain | protein | 212 | 3% helix, 50% strand | — |
| B | Antibody Fab fragment light chain | protein | 214 | 5% helix, 47% strand | — |
| C | Antibody Fab fragment heavy chain | protein | 213 | 3% helix, 50% strand | — |
| D | Antibody Fab fragment light chain | protein | 211 | 6% helix, 47% strand | — |
| E | Megakaryocyte and platelet inhibitory receptor G6B | protein | 99 | 0% helix, 29% strand | O95866 |
| F | Megakaryocyte and platelet inhibitory receptor G6B | protein | 98 | 0% helix, 35% strand | O95866 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 4 copies · chains E, F
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 4 copies · chains E, F
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains E, F
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.65 | 0.74 | 72 | empty |
| 2 | 304 | 0.64 | 0.80 | 47 | empty |
| 3 | 622 | 0.63 | 0.74 | 65 | empty |
| 4 | 341 | 0.58 | 0.76 | 43 | empty |
| 5 | 376 | 0.57 | 0.74 | 46 | IDS, SGN |
Interfaces
7 interfaces between chains.
- C–D · 1855 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1790 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 534 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 530 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 409 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
- 6R0X · The extracellular domain of G6b-B in complex with Fab fragment and DP12 heparin… · the same entry in another collection · chain F against F, TM-score 1.00
- O95866 · AlphaFold monomer V2.0 prediction for megakaryocyte and platelet inhibitory receptor G6B… · a predicted model of the same protein · chain E against A, TM-score 0.91
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 O95866
- Elsewhere: RCSB PDB 6R0X · PDBe 6R0X · UniProt O95866
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