Research workbench
High resolution crystal structure of human B7-2 igv domain in P21 space group
Analyse High resolution crystal structure of human B7-2 igv domain in P21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YXK
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-lymphocyte activation antigen CD86
- UniProt
- P42081
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | T-lymphocyte activation antigen CD86 | protein | 110 | 8% helix, 54% strand | P42081 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.62 | 0.76 | 54 | empty |
| 2 | 81 | 0.45 | 0.81 | 21 | empty |
| 3 | 68 | 0.35 | 0.78 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 575 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 523 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5YXK · High resolution crystal structure of Human B7-2 IgV domain in P21 space group · the same entry in another collection · chain D against D, TM-score 1.00
- P42081 · AlphaFold monomer V2.0 prediction for T-lymphocyte activation antigen CD86 (P42081) · 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 P42081
- Elsewhere: RCSB PDB 5YXK · PDBe 5YXK · UniProt P42081
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