Research workbench
Chimeric germline Fab 7G12 with jeffamine fragment bound
Analyse Chimeric germline Fab 7G12 with jeffamine fragment bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NGX
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germline metal chelatase catalytic antibody, light chain; Germline metal chelatase…
- Ligands
- JEF
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Germline metal chelatase catalytic antibody, light chain | protein | 213 | 6% helix, 50% strand | — |
| B, H | Germline metal chelatase catalytic antibody, heavy chain | protein | 216 | 8% helix, 47% strand | — |
Ligands and binding sites
- JEF · O-(O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500) · ligand · 2 copies · chains A, B, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.60 | 0.80 | 36 | empty |
| 2 | 225 | 0.59 | 0.80 | 39 | empty |
| 3 | 245 | 0.58 | 0.78 | 25 | JEF |
| 4 | 231 | 0.57 | 0.79 | 24 | JEF |
| 5 | 304 | 0.53 | 0.75 | 45 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1786 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1764 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1NGX · Chimeric Germline Fab 7g12 with jeffamine fragment bound · 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 1NGX · PDBe 1NGX
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