Research workbench
Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct
Analyse Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VW3
- Type
- protein + DNA
- Length
- 467 residues
- Chains
- 4
- 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…
- Ligands
- NCO
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) | protein | 215 | 7% helix, 52% strand | — |
| H | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain) | protein | 216 | 6% helix, 49% strand | — |
| A | DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY) P*AP*TP*GP*GP*AP*CP*GP*G)-3') | dna | 18 | — | — |
| B | DNA (5'- D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · chains H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.57 | 0.75 | 53 | empty |
| 2 | 114 | 0.46 | 0.79 | 18 | empty |
| 3 | 100 | 0.39 | 0.76 | 20 | empty |
| 4 | 133 | 0.37 | 0.73 | 17 | empty |
| 5 | 62 | 0.29 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1773 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 736 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- L–B · 417 Ų buried · 2 hydrogen bonds · protein-nucleic
- L–A · 351 Ų buried · 4 hydrogen bonds · protein-nucleic
- H–A · 334 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 3VW3 · Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct · 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 3VW3 · PDBe 3VW3
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