MolNFT v1 · #89960 · protein
Crystal structure of pika gitrl
4E4S · Tumor necrosis factor ligand superfamily member 18: “Crystal structure of pika gitrl”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.64). MolNFT v1 #89960 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4E4S
- Type
- protein
- Length
- 687 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 18
- Ligands
- MG
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 18 | protein | 113 | 5% helix, 52% strand | — |
| B | Tumor necrosis factor ligand superfamily member 18 | protein | 115 | 5% helix, 51% strand | — |
| C | Tumor necrosis factor ligand superfamily member 18 | protein | 114 | 5% helix, 52% strand | — |
| D | Tumor necrosis factor ligand superfamily member 18 | protein | 112 | 5% helix, 52% strand | — |
| E | Tumor necrosis factor ligand superfamily member 18 | protein | 119 | 3% helix, 50% strand | — |
| F | Tumor necrosis factor ligand superfamily member 18 | protein | 114 | 5% helix, 51% strand | — |
Ligands and binding sites
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 | 557 | 0.64 | 0.76 | 56 | GOL |
| 2 | 473 | 0.61 | 0.75 | 49 | GOL |
| 3 | 64 | 0.48 | 0.84 | 17 | empty |
| 4 | 90 | 0.43 | 0.79 | 13 | GOL |
| 5 | 151 | 0.42 | 0.74 | 26 | GOL |
Interfaces
7 interfaces between chains.
- A–F · 625 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 453 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 446 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 437 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 425 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4E4S · Crystal structure of Pika GITRL · 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 4E4S · PDBe 4E4S
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