Research workbench
Crystal structure of the CD27:CD70 co-stimulatory complex
Analyse Crystal structure of the CD27:CD70 co-stimulatory complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KX0
- Type
- protein
- Length
- 718 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD70 antigen; CD27 antigen
- UniProt
- P32970, P26842
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | CD70 antigen | protein | 140 | 4% helix, 51% strand | P32970 |
| D | CD27 antigen | protein | 100 | 0% helix, 35% strand | P26842 |
| E, F | CD27 antigen | protein | 99 | 0% helix, 35% strand | P26842 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, E, B, F, C, D
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.84 | 0.96 | 30 | TRS |
| 2 | 158 | 0.48 | 0.77 | 32 | empty |
| 3 | 162 | 0.48 | 0.77 | 33 | empty |
| 4 | 162 | 0.47 | 0.77 | 37 | empty |
| 5 | 60 | 0.47 | 0.84 | 18 | NAG |
Interfaces
9 interfaces between chains.
- A–B · 1092 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1089 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1085 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 766 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 756 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7KX0 · Crystal structure of the CD27:CD70 co-stimulatory complex · the same entry in another collection · chain F against F, TM-score 1.00
- P32970 · AlphaFold monomer V2.0 prediction for CD70 antigen (P32970) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P26842 · AlphaFold monomer V2.0 prediction for CD27 antigen (P26842) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 P32970
- Every structure of UniProt P26842
- Elsewhere: RCSB PDB 7KX0 · PDBe 7KX0 · UniProt P32970 · UniProt P26842
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