MolNFT v1 · #106223 · protein
Crystal structure of the light and hvem complex
4RSU · Tumor necrosis factor ligand superfamily member 14, soluble…: “Crystal structure of the light and hvem complex”. X-ray diffraction, 2 ligands (NAG, CL), 20 pockets (best druggability 0.83). MolNFT v1 #106223 on GenesisL1: 3D…
- PDB
- 4RSU
- Type
- protein
- Length
- 1,496 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 14, soluble form; Tumor necrosis factor…
- UniProt
- O43557, Q92956
- Ligands
- NAG, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 10 distinct chains · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 14, soluble form | protein | 149 | 2% helix, 50% strand | O43557 |
| B | Tumor necrosis factor ligand superfamily member 14, soluble form | protein | 142 | 2% helix, 53% strand | O43557 |
| C | Tumor necrosis factor ligand superfamily member 14, soluble form | protein | 138 | 2% helix, 53% strand | O43557 |
| D | Tumor necrosis factor receptor superfamily member 14 | protein | 105 | 3% helix, 46% strand | Q92956 |
| E | Tumor necrosis factor receptor superfamily member 14 | protein | 101 | 3% helix, 40% strand | Q92956 |
| F | Tumor necrosis factor receptor superfamily member 14 | protein | 98 | 3% helix, 37% strand | Q92956 |
| G, H | Tumor necrosis factor ligand superfamily member 14, soluble form | protein | 150 | 2% helix, 50% strand | O43557 |
| I | Tumor necrosis factor ligand superfamily member 14, soluble form | protein | 147 | 2% helix, 51% strand | O43557 |
| J, K | Tumor necrosis factor receptor superfamily member 14 | protein | 106 | 3% helix, 45% strand | Q92956 |
| L | Tumor necrosis factor receptor superfamily member 14 | protein | 104 | 3% helix, 46% strand | Q92956 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains D, E, J, K, L
- CL · Chloride ion · ion · 14 copies · chains A, D, B, C, F, E, G, J, L, H, I, K
- GOL · Glycerol · additive · 8 copies · chains B, C, E, A, D, F, G, H, J, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.83 | 0.85 | 110 | GOL |
| 2 | 1158 | 0.81 | 0.82 | 145 | CL, GOL |
| 3 | 684 | 0.76 | 0.81 | 92 | GOL |
| 4 | 812 | 0.75 | 0.80 | 82 | empty |
| 5 | 749 | 0.74 | 0.80 | 76 | empty |
Interfaces
26 interfaces between chains.
- H–I · 1159 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1071 Ų buried · 20 hydrogen bonds · protein-protein
- G–I · 1050 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 989 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 932 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4RSU · Crystal structure of the light and hvem complex · the same entry in another collection · chain L against L, 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 O43557
- Every structure of UniProt Q92956
- Elsewhere: RCSB PDB 4RSU · PDBe 4RSU · UniProt O43557 · UniProt Q92956
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