MolNFT v1 · #119958 · protein + DNA
Crystal structure of sle patient-derived anti-DNA antibody in complex with oligonucleotide
5GKR · IGG2, Fab (heavy chain): “Crystal structure of sle patient-derived anti-DNA antibody in complex with oligonucleotide”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #119958 on GenesisL1: 3D structure, binding…
- PDB
- 5GKR
- Type
- protein + DNA
- Length
- 831 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2, Fab (heavy chain); Lambda, Fab (light chain); DNA (5'-D(P*TP*TP*TP*T)-3')
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG2, Fab (heavy chain) | protein | 207 | 7% helix, 55% strand | — |
| B | Lambda, Fab (light chain) | protein | 213 | 7% helix, 50% strand | — |
| C | IGG2, Fab (heavy chain) | protein | 202 | 6% helix, 55% strand | — |
| D | Lambda, Fab (light chain) | protein | 206 | 7% helix, 51% strand | — |
| T | DNA (5'-D(P*TP*TP*TP*T)-3') | dna | 3 | — | — |
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 | 1149 | 0.73 | 0.76 | 90 | empty |
| 2 | 677 | 0.70 | 0.78 | 65 | empty |
| 3 | 71 | 0.38 | 0.78 | 19 | empty |
| 4 | 71 | 0.28 | 0.72 | 14 | empty |
| 5 | 50 | 0.26 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1830 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1775 Ų buried · 15 hydrogen bonds · protein-protein
- A–T · 385 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 222 Ų buried · 1 hydrogen bond · protein-protein
- B–T · 157 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5GKR · Crystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide · 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 5GKR · PDBe 5GKR
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