Research workbench
Chimeric affinity matured Fab 7G12 complexed with mesoporphyrin
Analyse Chimeric affinity matured Fab 7G12 complexed with mesoporphyrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NGW
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mature metal chelatase catalytic antibody, light chain; Mature metal chelatase catalytic…
- UniProt
- P06328
- Ligands
- MMP
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Mature metal chelatase catalytic antibody, light chain | protein | 213 | 7% helix, 51% strand | — |
| H, B | Mature metal chelatase catalytic antibody, heavy chain | protein | 216 | 6% helix, 49% strand | P06328 |
Ligands and binding sites
- MMP · N-methylmesoporphyrin · ligand · 2 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.63 | 0.75 | 69 | empty |
| 2 | 548 | 0.62 | 0.75 | 62 | empty |
| 3 | 139 | 0.51 | 0.80 | 23 | empty |
| 4 | 123 | 0.48 | 0.79 | 16 | empty |
| 5 | 72 | 0.42 | 0.80 | 17 | MMP |
Interfaces
2 interfaces between chains.
- A–B · 1837 Ų buried · 10 hydrogen bonds · protein-protein
- L–H · 1800 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1NGW · Chimeric Affinity Matured Fab 7g12 complexed with mesoporphyrin · the same entry in another collection · chain L against L, TM-score 1.00
- P06328 · AlphaFold monomer V2.0 prediction for ig heavy chain V region 1-72 (P06328) · a predicted model of the same protein · chain H against A, TM-score 0.45
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P06328
- Elsewhere: RCSB PDB 1NGW · PDBe 1NGW · UniProt P06328
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