MolNFT v1 · #78677 · protein
Crystal structure of mab 17.2 in complex with R13 peptide
3SGE · Light chain: “Crystal structure of mab 17.2 in complex with R13 peptide”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.77). MolNFT v1 #78677 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SGE
- Type
- protein
- Length
- 894 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain; R13 peptide
- Ligands
- CA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, I | Light chain | protein | 219 | 5% helix, 50% strand | — |
| H, J | Heavy chain | protein | 217 | 8% helix, 52% strand | — |
| K, M | R13 peptide | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains L, K, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.77 | 0.79 | 89 | empty |
| 2 | 550 | 0.62 | 0.74 | 56 | empty |
| 3 | 324 | 0.57 | 0.76 | 38 | CA |
| 4 | 85 | 0.53 | 0.85 | 22 | empty |
| 5 | 191 | 0.52 | 0.78 | 32 | empty |
Interfaces
10 interfaces between chains.
- L–H · 1836 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1740 Ų buried · 18 hydrogen bonds · protein-protein
- L–J · 613 Ų buried · 8 hydrogen bonds · protein-protein
- J–M · 587 Ų buried · 13 hydrogen bonds · protein-protein
- H–K · 524 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3SGE · Crystal structure of mAb 17.2 in complex with R13 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 3SGE · PDBe 3SGE
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