MolNFT v1 · #154510 · protein + DNA
Antibody 64M-5 Fab including isoasp in complex with DT(6-4)T
6KDI · Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain): “Antibody 64M-5 Fab including isoasp in complex with DT(6-4)T”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #154510 on GenesisL1: 3D structure, binding…
- PDB
- 6KDI
- Type
- protein + DNA
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain); Anti-(6-4) photoproduct…
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) | protein | 215 | 6% helix, 52% strand | — |
| H | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain) | protein | 217 | 7% helix, 52% strand | — |
| A | DNA (5'-D(*(64T)P*(5PY))-3') | dna | 2 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.62 | 0.74 | 63 | empty |
| 2 | 78 | 0.32 | 0.74 | 17 | empty |
| 3 | 54 | 0.29 | 0.75 | 16 | empty |
| 4 | 50 | 0.25 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1813 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 245 Ų buried · 5 hydrogen bonds · protein-nucleic
- L–A · 143 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 6KDI · Antibody 64M-5 Fab including isoAsp in complex with dT(6-4)T · the same entry in another collection · chain L against L, 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 6KDI · PDBe 6KDI
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