MolNFT v1 · #170039 · protein
Ab 5B1 bound to CA19-9
6XUN · Heavy chain: “Ab 5B1 bound to CA19-9”. X-ray diffraction, 4 ligands (NAG, GAL, SIA), 16 pockets (best druggability 0.66). MolNFT v1 #170039 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XUN
- Type
- protein
- Length
- 1,310 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain
- Ligands
- NAG, GAL, SIA, FUC
- Pockets
- 16 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain | protein | 220 | 5% helix, 52% strand | — |
| B, D, L | Light chain | protein | 217 | 6% helix, 50% strand | — |
| A | Heavy chain | protein | 218 | 9% helix, 53% strand | — |
| C | Heavy chain | protein | 221 | 8% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains H, L, B, A, D, C
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains H, L, B, A, D, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains H, L, B, A, D, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains H, L, B, A, D, C
- GOL · Glycerol · additive · 4 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.66 | 0.75 | 60 | empty |
| 2 | 631 | 0.64 | 0.75 | 65 | GOL |
| 3 | 561 | 0.61 | 0.74 | 54 | empty |
| 4 | 570 | 0.61 | 0.74 | 59 | empty |
| 5 | 50 | 0.53 | 0.89 | 21 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1749 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 1717 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 1695 Ų buried · 14 hydrogen bonds · protein-protein
- D–L · 617 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 450 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6XUN · Ab 5b1 bound to CA19-9 · 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 6XUN · PDBe 6XUN
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