MolNFT v1 · #12357 · protein + DNA
Antibody 64M-2 Fab complexed with DTT(6-4)TT
1KEG · 5'-D(*TP*(64T)P*TP*T)-3': “Antibody 64M-2 Fab complexed with DTT(6-4)TT”. X-ray diffraction, 1 ligand (NI), 3 pockets (best druggability 0.44). MolNFT v1 #12357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KEG
- Type
- protein + DNA
- Length
- 436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*(64T)P*TP*T)-3'; Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain)…
- Ligands
- NI
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*TP*(64T)P*TP*T)-3' | dna | 4 | — | — |
| L | Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain) | protein | 216 | 6% helix, 51% strand | — |
| H | Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain) | protein | 216 | 7% helix, 51% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.44 | 0.74 | 33 | empty |
| 2 | 63 | 0.29 | 0.74 | 15 | empty |
| 3 | 63 | 0.27 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1796 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 335 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–L · 280 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 1KEG · Antibody 64M-2 Fab complexed with dTT(6-4)TT · 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 1KEG · PDBe 1KEG
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