Research workbench
Crystal structure of mouse RP105/MD-1 complex
Analyse Crystal structure of mouse RP105/MD-1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T6Q
- Type
- protein
- Length
- 1,480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD180 antigen; Lymphocyte antigen 86
- UniProt
- Q62192, O88188
- Ligands
- NAG, MAN, BMA, CU
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CD180 antigen | protein | 601 | 13% helix, 20% strand | Q62192 |
| C, D | Lymphocyte antigen 86 | protein | 139 | 0% helix, 57% strand | O88188 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains C, A, D, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C, D
- CU · Copper (II) ion · metal · chains A
- GOL · Glycerol · additive · 15 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.85 | 0.86 | 113 | GOL |
| 2 | 707 | 0.83 | 0.86 | 51 | empty |
| 3 | 645 | 0.82 | 0.85 | 53 | empty |
| 4 | 659 | 0.67 | 0.76 | 83 | MAN |
| 5 | 263 | 0.60 | 0.80 | 32 | GOL |
Interfaces
5 interfaces between chains.
- B–D · 1000 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 999 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 605 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 587 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 371 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 3T6Q · Crystal structure of mouse RP105/MD-1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q62192 · AlphaFold monomer V2.0 prediction for CD180 antigen (Q62192) · a predicted model of the same protein · chain B against A, TM-score 0.99
- O88188 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 86 (O88188) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q62192
- Every structure of UniProt O88188
- Elsewhere: RCSB PDB 3T6Q · PDBe 3T6Q · UniProt Q62192 · UniProt O88188
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