MolNFT v1 · #58395 · protein
Crystal structure of human RP105/MD-1 complex
3B2D · CD180 antigen: “Crystal structure of human RP105/MD-1 complex”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 10 pockets (best druggability 0.87). MolNFT v1 #58395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3B2D
- 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
- Q99467, O95711
- Ligands
- MAN, NAG, BMA
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CD180 antigen | protein | 601 | 10% helix, 19% strand | Q99467 |
| C, D | Lymphocyte antigen 86 | protein | 139 | 0% helix, 52% strand | O95711 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains C, A, D, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.87 | 0.88 | 110 | empty |
| 2 | 769 | 0.85 | 0.87 | 61 | empty |
| 3 | 725 | 0.83 | 0.86 | 56 | empty |
| 4 | 467 | 0.64 | 0.77 | 56 | empty |
| 5 | 576 | 0.64 | 0.75 | 73 | MAN |
Interfaces
5 interfaces between chains.
- A–C · 985 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 982 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 666 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 646 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3B2D · Crystal structure of human RP105/MD-1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q99467 · AlphaFold monomer V2.0 prediction for CD180 antigen (Q99467) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O95711 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 86 (O95711) · 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 Q99467
- Every structure of UniProt O95711
- Elsewhere: RCSB PDB 3B2D · PDBe 3B2D · UniProt Q99467 · UniProt O95711
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