MolNFT v1 · #94572 · protein
HLA-do in complex with HLA-dm
4I0P · HLA-dma protein: “HLA-do in complex with HLA-dm”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.78). MolNFT v1 #94572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4I0P
- Type
- protein
- Length
- 1,488 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-dma protein; HLA class II histocompatibility antigen, dm beta chain; HLA class II…
- UniProt
- Q6ICR9, P28068, P06340, P13765
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | HLA-dma protein | protein | 188 | 13% helix, 47% strand | Q6ICR9 |
| B | HLA class II histocompatibility antigen, dm beta chain | protein | 186 | 21% helix, 44% strand | P28068 |
| C, G | HLA class II histocompatibility antigen, do alpha chain | protein | 181 | 12% helix, 45% strand | P06340 |
| D | HLA class II histocompatibility antigen, do beta chain | protein | 188 | 20% helix, 43% strand | P13765 |
| F | HLA class II histocompatibility antigen, dm beta chain | protein | 187 | 16% helix, 43% strand | P28068 |
| H | HLA class II histocompatibility antigen, do beta chain | protein | 189 | 20% helix, 44% strand | P13765 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 3 copies · chains D, E, F, G, H
- PGE · Triethylene glycol · additive · chains D, H
- ACT · Acetate ion · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.78 | 0.79 | 100 | empty |
| 2 | 1145 | 0.77 | 0.79 | 104 | GOL |
| 3 | 143 | 0.65 | 0.87 | 23 | empty |
| 4 | 144 | 0.65 | 0.87 | 22 | empty |
| 5 | 481 | 0.60 | 0.74 | 46 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2936 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 2930 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 2720 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 2695 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 1002 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 4I0P · HLA-DO in complex with HLA-DM · the same entry in another collection · chain H against H, TM-score 1.00
- P06340 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, do alpha… · a predicted model of the same protein · chain C against A, TM-score 0.94
- P28068 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dm beta… · a predicted model of the same protein · chain F against A, TM-score 0.92
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 Q6ICR9
- Every structure of UniProt P28068
- Every structure of UniProt P06340
- Every structure of UniProt P13765
- Elsewhere: RCSB PDB 4I0P · PDBe 4I0P · UniProt Q6ICR9 · UniProt P28068 · UniProt P06340 · UniProt P13765
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