MolNFT v1 · #170036 · protein
Ablift design 15 of ab 1116NS19.9
6XUK · Heavy chain: “Ablift design 15 of ab 1116NS19.9”. X-ray diffraction, 4 ligands (NAG, GAL, SIA), 5 pockets (best druggability 0.59). MolNFT v1 #170036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XUK
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain
- Ligands
- NAG, GAL, SIA, FUC
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain | protein | 216 | 10% helix, 51% strand | — |
| L | Light chain | protein | 214 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- GAL · beta-D-galactopyranose · sugar · chains H, L
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains H, L
- FUC · alpha-L-fucopyranose · sugar · chains H, L
- GOL · Glycerol · additive · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.59 | 0.74 | 59 | empty |
| 2 | 299 | 0.58 | 0.77 | 38 | empty |
| 3 | 66 | 0.33 | 0.75 | 15 | SIA |
| 4 | 75 | 0.30 | 0.73 | 19 | empty |
| 5 | 62 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 1641 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6XUK · AbLIFT design 15 of Ab 1116NS19.9 · the same entry in another collection · chain H against H, 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 6XUK · PDBe 6XUK
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