Research workbench
The nz-1 Fab complexed with the PDZ tandem fragment of a. aeolicus S2P homolog with the PA12 tag inserted between the residues 181 and 186
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
- 6ICC
- Type
- protein
- Length
- 617 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PDZ tandem fragment with pa tag; Heavy chain of antigen binding fragment, Fab of nz-1…
- EC
- 3.4.24.-
- UniProt
- O67776
- Ligands
- SNN
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PDZ tandem fragment with pa tag (EC 3.4.24.-) | protein | 184 | 22% helix, 30% strand | O67776 |
| H | Heavy chain of antigen binding fragment, Fab of nz-1 | protein | 219 | 10% helix, 53% strand | — |
| L | Light chain of antigen binding fragment, Fab of nz-1 | protein | 214 | 9% helix, 52% strand | — |
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
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.61 | 0.74 | 64 | empty |
| 2 | 215 | 0.50 | 0.76 | 29 | empty |
| 3 | 115 | 0.48 | 0.79 | 16 | empty |
| 4 | 162 | 0.45 | 0.75 | 21 | empty |
| 5 | 114 | 0.43 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1818 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 610 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 366 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent, 1 modified (disulfide, covalent ligand, cyclization).
Compared structures
- 6ICC · The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the… · the same entry in another collection · chain A against A, 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 0.52
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
- Elsewhere: RCSB PDB 6ICC · PDBe 6ICC · UniProt O67776
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