Research workbench
High resolution crystal structures of thymus and activation-regulated chemokine
Analyse High resolution crystal structures of thymus and activation-regulated chemokine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NR4
- Type
- protein
- Length
- 524 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymus and activation-regulated chemokine
- UniProt
- Q92583
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymus and activation-regulated chemokine | protein | 67 | 22% helix, 28% strand | Q92583 |
| B | Thymus and activation-regulated chemokine | protein | 64 | 27% helix, 30% strand | Q92583 |
| C | Thymus and activation-regulated chemokine | protein | 66 | 23% helix, 32% strand | Q92583 |
| D | Thymus and activation-regulated chemokine | protein | 63 | 25% helix, 32% strand | Q92583 |
| E | Thymus and activation-regulated chemokine | protein | 69 | 25% helix, 28% strand | Q92583 |
| F | Thymus and activation-regulated chemokine | protein | 66 | 26% helix, 29% strand | Q92583 |
| G | Thymus and activation-regulated chemokine | protein | 66 | 23% helix, 27% strand | Q92583 |
| H | Thymus and activation-regulated chemokine | protein | 63 | 27% helix, 29% strand | Q92583 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.73 | 0.77 | 67 | empty |
| 2 | 158 | 0.52 | 0.79 | 23 | SO4 |
| 3 | 111 | 0.42 | 0.76 | 25 | empty |
| 4 | 97 | 0.40 | 0.77 | 17 | empty |
| 5 | 81 | 0.35 | 0.76 | 20 | empty |
Interfaces
7 interfaces between chains.
- E–F · 887 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 886 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 834 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 810 Ų buried · 16 hydrogen bonds · protein-protein
- D–G · 350 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1NR4 · High resolution crystal structures of thymus and activation-regulated chemokine · the same entry in another collection · chain G against G, TM-score 1.00
- Q92583 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 17 (Q92583) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q92583
- Elsewhere: RCSB PDB 1NR4 · PDBe 1NR4 · UniProt Q92583
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