MolNFT v1 · #175424 · protein
The nz-1 Fab complexed with the PDZ tandem fragment of a. aeolicus S2P homolog with the PA14 tag inserted between the residues 235 and 236
7CQD · Heavy chain of antigen binding fragment, Fab of nz-1: “The nz-1 Fab complexed with the PDZ tandem fragment of a. aeolicus S2P homolog with the PA14 tag inserted…”. X-ray diffraction, 11 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 7CQD
- Type
- protein
- Length
- 1,040 residues
- Chains
- 6
- 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
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of antigen binding fragment, Fab of nz-1 | protein | 209 | 5% helix, 54% strand | — |
| L, M | Light chain of antigen binding fragment, Fab of nz-1 | protein | 214 | 9% helix, 52% strand | — |
| A, B | Putative zinc metalloprotease AQ_1964,PA14 from podoplanin, putative zinc metalloprotease AQ_1964 | protein | 97 | 14% helix, 33% strand | O67776, Q86YL7 |
| I | Heavy chain of antigen binding fragment, Fab of nz-1 | protein | 209 | 7% helix, 52% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.77 | 0.79 | 115 | empty |
| 2 | 447 | 0.71 | 0.82 | 59 | empty |
| 3 | 362 | 0.52 | 0.73 | 45 | empty |
| 4 | 55 | 0.44 | 0.84 | 17 | empty |
| 5 | 91 | 0.43 | 0.79 | 13 | empty |
Interfaces
9 interfaces between chains.
- M–I · 1801 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1680 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 656 Ų buried · 14 hydrogen bonds · protein-protein
- I–B · 635 Ų buried · 13 hydrogen bonds · protein-protein
- L–B · 623 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 7CQD · The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the… · the same entry in another collection · chain B against B, 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 0.81
- Q86YL7 · AlphaFold monomer V2.0 prediction for podoplanin (Q86YL7) · a predicted model of the same protein · chain A against A, TM-score 0.19
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 7CQD · PDBe 7CQD · UniProt O67776 · UniProt Q86YL7
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