Research workbench
Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin
Analyse Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DNF
- Type
- protein
- Length
- 585 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.549
- Source
- Homo sapiens
- Molecule
- C-C motif chemokine 5
- UniProt
- P13501
- Ligands
- SGN, GLA, BGC, IDS, CL, SO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.549 · 1 distinct chain · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | C-C motif chemokine 5 | protein | 65 | 22% helix, 29% strand | P13501 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 6 copies · chains C, D, I
- GLA · alpha-D-galactopyranose · sugar · 6 copies · chains A, D, C, F, H, I
- BGC · beta-D-glucopyranose · sugar · 5 copies · chains A, D, C, F, E, G, H, I
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 3 copies · chains C, D, I
- CL · Chloride ion · ion · 20 copies · chains A, B, C, D, E, F, G, H, I
- SO4 · Sulfate ion · ion · 5 copies · chains A, E, F, G, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.62 | 0.82 | 31 | GLA, BGC |
| 2 | 204 | 0.60 | 0.81 | 34 | GLA, BGC |
| 3 | 186 | 0.52 | 0.78 | 28 | BGC, GLA |
| 4 | 80 | 0.48 | 0.83 | 25 | empty |
| 5 | 50 | 0.45 | 0.85 | 17 | CL |
Interfaces
13 interfaces between chains.
- E–F · 775 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 770 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 729 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 666 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, O-glycosylation).
Compared structures
- 5DNF · Crystal structure of cc chemokine 5 (CCL5) oligomer in complex with heparin · the same entry in another collection · chain I against I, TM-score 1.00
- P13501 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 5 (P13501) · a predicted model of the same protein · chain I against A, TM-score 0.95
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 P13501
- Elsewhere: RCSB PDB 5DNF · PDBe 5DNF · UniProt P13501
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