Research workbench
Crystal structure of monoclonal antibody 2D12.5 Fab complexed with Y- dota
Analyse Crystal structure of monoclonal antibody 2D12.5 Fab complexed with Y- dota in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NC2
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody 2D12.5, lambda light chain; Monoclonal antibody 2D12.5, IGG1 gamma…
- Ligands
- DOE, NAG, YT3, CL
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monoclonal antibody 2D12.5, lambda light chain | protein | 211 | 8% helix, 53% strand | — |
| B | Monoclonal antibody 2D12.5, IGG1 gamma heavy chain | protein | 219 | 7% helix, 49% strand | — |
| C | Monoclonal antibody 2D12.5, lambda light chain | protein | 215 | 7% helix, 52% strand | — |
| D | Monoclonal antibody 2D12.5, IGG1 gamma heavy chain | protein | 215 | 7% helix, 52% strand | — |
Ligands and binding sites
- DOE · (S)-2-(4-(2-(2-hydroxyethylthio)-acetamido)-benzyl)-1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetate · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
- YT3 · Yttrium (III) ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · 2 copies
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 | 942 | 0.69 | 0.74 | 78 | empty |
| 2 | 689 | 0.65 | 0.75 | 59 | empty |
| 3 | 370 | 0.56 | 0.75 | 34 | empty |
| 4 | 120 | 0.45 | 0.78 | 19 | empty |
| 5 | 120 | 0.41 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2073 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1897 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 236 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1NC2 · Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y-DOTA · 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 1NC2 · PDBe 1NC2
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