MolNFT v1 · #113853 · protein
Crystal structure of a Fab fragment with the ligand peptide
5AUM · Heavy chain of Fab fragment: “Crystal structure of a Fab fragment with the ligand peptide”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.77). MolNFT v1 #113853 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5AUM
- Type
- protein
- Length
- 871 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment; Light chain of Fab fragment; Peptide renlyfqgkdg
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of Fab fragment | protein | 208 | 12% helix, 52% strand | — |
| A | Heavy chain of Fab fragment | protein | 209 | 7% helix, 54% strand | — |
| B, L | Light chain of Fab fragment | protein | 216 | 5% helix, 53% strand | — |
| C, D | Peptide renlyfqgkdg | protein | 11 | 45% helix, 9% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.77 | 0.80 | 123 | empty |
| 2 | 171 | 0.56 | 0.81 | 29 | empty |
| 3 | 57 | 0.48 | 0.85 | 21 | empty |
| 4 | 147 | 0.43 | 0.75 | 27 | empty |
| 5 | 139 | 0.40 | 0.74 | 29 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1664 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1642 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 856 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 614 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 613 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5AUM · Crystal structure of a Fab fragment with the ligand peptide · 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 5AUM · PDBe 5AUM
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