MolNFT v1 · #52070 · protein
Anti trimeric lewis X FAB54-5C10-a
2VQ1 · IGKV1-117 protein: “Anti trimeric lewis X FAB54-5C10-a”. X-ray diffraction, 2 ligands (GLY, AZI), 8 pockets (best druggability 0.71). MolNFT v1 #52070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VQ1
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGKV1-117 protein; Anti-human Fc gamma receptor III 3G8 gamma heavy chain variable region
- Ligands
- GLY, AZI
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | IGKV1-117 protein | protein | 216 | 6% helix, 54% strand | — |
| B | Anti-human Fc gamma receptor III 3G8 gamma heavy chain variable region | protein | 213 | 7% helix, 53% strand | — |
| F | Anti-human Fc gamma receptor III 3G8 gamma heavy chain variable region | protein | 211 | 6% helix, 50% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 8 copies · chains A, B, E, F
- AZI · Azide ion · ion · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.71 | 0.77 | 84 | GLY, GOL |
| 2 | 769 | 0.67 | 0.75 | 65 | AZI |
| 3 | 368 | 0.56 | 0.75 | 37 | empty |
| 4 | 86 | 0.37 | 0.76 | 19 | GLY |
| 5 | 97 | 0.33 | 0.73 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1819 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1794 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 202 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 197 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2VQ1 · anti trimeric Lewis X Fab54-5C10-A · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 2VQ1 · PDBe 2VQ1
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