Research workbench
NVPIZZA2-H16S58 with cobalt
Analyse NVPIZZA2-H16S58 with cobalt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I1Y
- Type
- protein
- Length
- 257 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NVPIZZ2A-H16S58
- Ligands
- CO, SO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NVPIZZ2A-H16S58 | protein | 86 | 3% helix, 40% strand | — |
| B | NVPIZZ2A-H16S58 | protein | 85 | 7% helix, 42% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.71 | 0.82 | 43 | empty |
| 2 | 69 | 0.40 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 753 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 636 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5I1Y · NvPizza2-H16S58 with cobalt · 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 5I1Y · PDBe 5I1Y
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