MolNFT v1 · #14543 · protein
Three-dimensional structure of a human immunoglobulin with a hinge deletion
1MCO · IGG1 mcg intact antibody (light chain): “Three-dimensional structure of a human immunoglobulin with a hinge deletion”. X-ray diffraction, 7 ligands (GUP, NAG, BMA), 6 pockets (best druggability 0.74). MolNFT v1 #14543 on GenesisL1…
- PDB
- 1MCO
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1 mcg intact antibody (light chain); IGG1 mcg intact antibody (heavy chain)
- Ligands
- GUP, NAG, BMA, MAN, GAL, SIA, FUL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1 mcg intact antibody (light chain) | protein | 216 | 5% helix, 44% strand | — |
| H | IGG1 mcg intact antibody (heavy chain) | protein | 428 | 4% helix, 35% strand | — |
Ligands and binding sites
- GUP · alpha-L-gulopyranose · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H
- BMA · beta-D-mannopyranose · sugar · chains H
- MAN · alpha-D-mannopyranose · sugar · chains H
- GAL · beta-D-galactopyranose · sugar · chains H
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains H
- FUL · beta-L-fucopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.74 | 0.77 | 79 | empty |
| 2 | 518 | 0.63 | 0.75 | 62 | empty |
| 3 | 82 | 0.58 | 0.87 | 22 | empty |
| 4 | 117 | 0.47 | 0.78 | 16 | empty |
| 5 | 179 | 0.46 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- L–H · 1792 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1MCO · Three-dimensional structure of a human immunoglobulin with a hinge deletion · 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 1MCO · PDBe 1MCO
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