MolNFT v1 · #119959 · protein
Crystal structure of sle patient-derived anti-DNA antibody
5GKS · IGG2, Fab (heavy chain): “Crystal structure of sle patient-derived anti-DNA antibody”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.74). MolNFT v1 #119959 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5GKS
- Type
- protein
- Length
- 826 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2, Fab (heavy chain); Lambda, Fab (light chain)
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG2, Fab (heavy chain) | protein | 206 | 9% helix, 53% strand | — |
| B | Lambda, Fab (light chain) | protein | 211 | 6% helix, 51% strand | — |
| C | IGG2, Fab (heavy chain) | protein | 200 | 8% helix, 55% strand | — |
| D | Lambda, Fab (light chain) | protein | 209 | 7% helix, 51% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
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 | 1148 | 0.74 | 0.77 | 98 | empty |
| 2 | 672 | 0.67 | 0.76 | 52 | empty |
| 3 | 162 | 0.47 | 0.76 | 30 | empty |
| 4 | 74 | 0.33 | 0.75 | 19 | empty |
| 5 | 70 | 0.29 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1793 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1746 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 848 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5GKS · Crystal structure of SLE patient-derived anti-DNA antibody · 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 5GKS · PDBe 5GKS
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