MolNFT v1 · #18761 · protein
Structural basis of peptide-carbohydrate mimicry in an antibody combining site
1PZ5 · Light chain of Fab (SYA/J6): “Structural basis of peptide-carbohydrate mimicry in an antibody combining site”. X-ray diffraction, 5 pockets (best druggability 0.65). MolNFT v1 #18761 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1PZ5
- Type
- protein
- Length
- 443 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab (SYA/J6); Heavy chain of Fab (SYA/J6); Octapeptide (mdwnmhaa)
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain of Fab (SYA/J6) | protein | 215 | 7% helix, 53% strand | — |
| B | Heavy chain of Fab (SYA/J6) | protein | 220 | 11% helix, 51% strand | — |
| C | Octapeptide (mdwnmhaa) | protein | 8 | 0% helix, 0% strand | — |
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 | 702 | 0.65 | 0.74 | 77 | empty |
| 2 | 121 | 0.53 | 0.82 | 20 | empty |
| 3 | 124 | 0.44 | 0.76 | 25 | empty |
| 4 | 79 | 0.34 | 0.75 | 17 | empty |
| 5 | 59 | 0.28 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1709 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 298 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1PZ5 · Structural basis of peptide-carbohydrate mimicry in an antibody combining site · the same entry in another collection · chain A against A, 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 1PZ5 · PDBe 1PZ5
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