MolNFT v1 · #171365 · protein
Engineered lipocalin C3A5 in complex with a transition state analog
6Z2C · Neutrophil gelatinase-associated lipocalin: “Engineered lipocalin C3A5 in complex with a transition state analog”. X-ray diffraction, 1 ligand (Q5E), 7 pockets (best druggability 0.76). MolNFT v1 #171365 on GenesisL1: 3D structure…
- PDB
- 6Z2C
- Type
- protein
- Length
- 531 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- Q5E
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 178 | 15% helix, 41% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 177 | 15% helix, 41% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 176 | 15% helix, 41% strand | P80188 |
Ligands and binding sites
- Q5E · 1,7,8,9,10,10-hexachloro-4-carboxypentyl-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-ene-3,5-dione · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.76 | 0.86 | 47 | empty |
| 2 | 367 | 0.74 | 0.85 | 28 | Q5E |
| 3 | 383 | 0.74 | 0.84 | 24 | Q5E |
| 4 | 326 | 0.73 | 0.85 | 23 | Q5E |
| 5 | 331 | 0.67 | 0.82 | 41 | empty |
Interfaces
3 interfaces between chains.
- B–C · 392 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 346 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 310 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6Z2C · Engineered lipocalin C3A5 in complex with a transition state analog · the same entry in another collection · chain B against B, 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
- Every structure of UniProt P80188
- Elsewhere: RCSB PDB 6Z2C · PDBe 6Z2C · UniProt P80188
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.