Research workbench
Cryo-EM structure of the human chemokine receptor CCR6 in complex with CCL20 and a go protein
Analyse Cryo-EM structure of the human chemokine receptor CCR6 in complex with CCL20… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WWZ
- Type
- protein
- Length
- 1,211 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1; C-C motif chemokine 20…
- UniProt
- P54311, P78556, P09471, P51684
- Pockets
- 13 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 47% strand | P54311 |
| C | C-C motif chemokine 20 | protein | 66 | 18% helix, 11% strand | P78556 |
| Y | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 55% helix, 0% strand | — |
| A | Guanine nucleotide-binding protein G(O) subunit alpha, guanine nucleotide-binding protein G(O) subunit alpha | protein | 210 | 40% helix, 17% strand | P09471 |
| S | SCFV16 | protein | 231 | 0% helix, 45% strand | — |
| R | C-C chemokine receptor type 6,C-C chemokine receptor type 6 | protein | 310 | 76% helix, 3% strand | P51684 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.85 | 0.86 | 79 | empty |
| 2 | 1188 | 0.81 | 0.82 | 67 | empty |
| 3 | 663 | 0.71 | 0.78 | 71 | empty |
| 4 | 753 | 0.70 | 0.77 | 74 | empty |
| 5 | 61 | 0.61 | 0.91 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–Y · 2142 Ų buried · 6 hydrogen bonds · protein-protein
- C–R · 1391 Ų buried · 12 hydrogen bonds · protein-protein
- A–R · 1289 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 1098 Ų buried · 8 hydrogen bonds · protein-protein
- A–S · 541 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6WWZ · Cryo-EM structure of the human chemokine receptor CCR6 in complex with CCL20 and a Go… · the same entry in another collection · chain R against R, TM-score 1.00
- P54311 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P78556 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 20 (P78556) · a predicted model of the same protein · chain C against A, TM-score 0.89
- P51684 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 6 (P51684) · a predicted model of the same protein · chain R against A, TM-score 0.87
- P09471 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(O) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.75
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 P54311
- Every structure of UniProt P78556
- Every structure of UniProt P09471
- Every structure of UniProt P51684
- Elsewhere: RCSB PDB 6WWZ · PDBe 6WWZ · UniProt P54311 · UniProt P78556 · UniProt P09471 · UniProt P51684
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