MolNFT v1 · #143245 · protein
HLA-DRB1*1402 in complex with citrullinated fibrinogen peptide
6ATZ · HLA class II histocompatibility antigen, dr alpha chain: “HLA-DRB1*1402 in complex with citrullinated fibrinogen peptide”. X-ray diffraction, 2 ligands (CIR, NAG), 10 pockets (best druggability 0.72). MolNFT v1 #143245 on GenesisL1…
- PDB
- 6ATZ
- Type
- protein
- Length
- 751 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; MHC class II antigen; Fibrinogen…
- UniProt
- P01903, A0A0A1I7H6
- Ligands
- CIR, NAG
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class II histocompatibility antigen, dr alpha chain | protein | 177 | 14% helix, 47% strand | P01903 |
| B | MHC class II antigen | protein | 188 | 18% helix, 46% strand | A0A0A1I7H6 |
| D | MHC class II antigen | protein | 187 | 18% helix, 46% strand | A0A0A1I7H6 |
| E, F | Fibrinogen beta chain | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, B, E, C, D, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.72 | 0.84 | 32 | empty |
| 2 | 406 | 0.72 | 0.83 | 36 | B3P |
| 3 | 819 | 0.67 | 0.74 | 71 | empty |
| 4 | 816 | 0.67 | 0.74 | 57 | empty |
| 5 | 453 | 0.54 | 0.72 | 48 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2369 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2349 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 622 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 531 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 530 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent, 4 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6ATZ · HLA-DRB1*1402 in complex with citrullinated fibrinogen peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A 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 P01903
- Every structure of UniProt A0A0A1I7H6
- Elsewhere: RCSB PDB 6ATZ · PDBe 6ATZ · UniProt P01903 · UniProt A0A0A1I7H6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.