MolNFT v1 · #121661 · protein
Structure of NVPIZZA2-H16S58
5I1Z: “Structure of NVPIZZA2-H16S58”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.81). MolNFT v1 #121661 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I1Z
- Type
- protein
- Length
- 1,525 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NVPIZZA2-H16S58
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, G, J, L, P | NVPIZZA2-H16S58 | protein | 85 | 4% helix, 40% strand | — |
| C, E, I, K, N, R | NVPIZZA2-H16S58 | protein | 84 | 4% helix, 38% strand | — |
| H | NVPIZZA2-H16S58 | protein | 83 | 4% helix, 43% strand | — |
| M, O, Q | NVPIZZA2-H16S58 | protein | 86 | 3% helix, 40% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, F, J, D, E, G, H, I, L, K, M, P, N, O, R, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.81 | 0.84 | 102 | SO4 |
| 2 | 903 | 0.80 | 0.83 | 93 | empty |
| 3 | 232 | 0.73 | 0.89 | 49 | SO4 |
| 4 | 499 | 0.73 | 0.82 | 47 | empty |
| 5 | 219 | 0.73 | 0.89 | 41 | SO4 |
Interfaces
41 interfaces between chains.
- M–P · 788 Ų buried · 7 hydrogen bonds · protein-protein
- P–Q · 767 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 764 Ų buried · 7 hydrogen bonds · protein-protein
- G–J · 742 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 728 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5I1Z · Structure of nvPizza2-H16S58 · 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 5I1Z · PDBe 5I1Z
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