MolNFT v1 · #143370 · protein
Crystal structure of FAB317 complex
6AXL · FAB317 light chains: “Crystal structure of FAB317 complex”. X-ray diffraction, 2 ligands (ACE, NH2), 8 pockets (best druggability 0.70). MolNFT v1 #143370 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AXL
- Type
- protein
- Length
- 882 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAB317 light chains; FAB317 heavy chain; Peptide…
- Ligands
- ACE, NH2
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B | FAB317 light chains | protein | 213 | 6% helix, 51% strand | — |
| D | FAB317 heavy chain | protein | 214 | 9% helix, 50% strand | — |
| A | FAB317 heavy chain | protein | 218 | 10% helix, 50% strand | — |
| G, I | Peptide ACE-asn-pro-asn-ala-asn-pro-asn-ala-asn-pro-asn- ala-NH2 | protein | 12 | 25% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, G, D, I
- NH2 · Amino group · ion · 2 copies · chains D, G, A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.70 | 0.96 | 24 | empty |
| 2 | 55 | 0.57 | 0.91 | 21 | empty |
| 3 | 295 | 0.51 | 0.74 | 48 | empty |
| 4 | 208 | 0.51 | 0.76 | 33 | empty |
| 5 | 245 | 0.49 | 0.74 | 39 | empty |
Interfaces
11 interfaces between chains.
- B–A · 1804 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1709 Ų buried · 11 hydrogen bonds · protein-protein
- A–I · 432 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 431 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 339 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6AXL · Crystal structure of Fab317 complex · the same entry in another collection · chain C against C, 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 6AXL · PDBe 6AXL
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