Research workbench
The nz-1 Fab complexed with the PDZ tandem fragment of a. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184
Analyse The nz-1 Fab complexed with the PDZ tandem fragment of a. aeolicus S2P homolog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CQC
- Type
- protein
- Length
- 612 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of antigen binding fragment, Fab of nz-1; Light chain of antigen binding…
- UniProt
- O67776, Q86YL7
- Ligands
- SNN
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of antigen binding fragment, Fab of nz-1 | protein | 212 | 8% helix, 54% strand | — |
| L | Light chain of antigen binding fragment, Fab of nz-1 | protein | 214 | 7% helix, 51% strand | — |
| A | Putative zinc metalloprotease AQ_1964,PA14 from podoplanin, putative zinc metalloprotease AQ_1964 | protein | 186 | 15% helix, 28% strand | O67776, Q86YL7 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.59 | 0.74 | 57 | empty |
| 2 | 465 | 0.55 | 0.73 | 53 | empty |
| 3 | 181 | 0.52 | 0.78 | 20 | empty |
| 4 | 82 | 0.44 | 0.79 | 17 | empty |
| 5 | 78 | 0.42 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1824 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 689 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 486 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent, 1 modified (disulfide, covalent ligand, cyclization).
Compared structures
- 7CQC · The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the… · the same entry in another collection · chain H against H, TM-score 1.00
- O67776 · AlphaFold monomer V2.0 prediction for putative zinc metalloprotease AQ_1964 (O67776) · a predicted model of the same protein · chain A against A, TM-score 0.88
- Q86YL7 · AlphaFold monomer V2.0 prediction for podoplanin (Q86YL7) · a predicted model of the same protein · chain A against A, TM-score 0.16
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 O67776
- Every structure of UniProt Q86YL7
- Elsewhere: RCSB PDB 7CQC · PDBe 7CQC · UniProt O67776 · UniProt Q86YL7
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