MolNFT v1 · #155639 · protein
Structure of antibody C9 in complex with methylated peptide
6LDW · Fab light chain: “Structure of antibody C9 in complex with methylated peptide”. X-ray diffraction, 2 ligands (NA, CL), 8 pockets (best druggability 0.63). MolNFT v1 #155639 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6LDW
- Type
- protein
- Length
- 837 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain; Ile-phe-glu-lys-phe-gly-M3L-gly-gly
- Ligands
- NA, CL
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab light chain | protein | 212 | 8% helix, 54% strand | — |
| H | Fab heavy chain | protein | 198 | 6% helix, 53% strand | — |
| B | Fab heavy chain | protein | 197 | 6% helix, 52% strand | — |
| D, C | Ile-phe-glu-lys-phe-gly-M3L-gly-gly | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.63 | 0.74 | 69 | empty |
| 2 | 529 | 0.60 | 0.74 | 57 | empty |
| 3 | 70 | 0.51 | 0.85 | 22 | empty |
| 4 | 66 | 0.49 | 0.85 | 22 | empty |
| 5 | 89 | 0.36 | 0.75 | 15 | CL |
Interfaces
7 interfaces between chains.
- A–B · 1634 Ų buried · 6 hydrogen bonds · protein-protein
- L–H · 1628 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 395 Ų buried · 3 hydrogen bonds · protein-protein
- L–C · 375 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 356 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 modified (disulfide, methylation).
Compared structures
- 6LDW · Structure of antibody C9 in complex with methylated peptide · 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 6LDW · PDBe 6LDW
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