Research workbench
HLA-DRB1*1402 in complex with VIMENTIN59-71
Analyse HLA-DRB1*1402 in complex with VIMENTIN59-71 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ATF
- Type
- protein
- Length
- 763 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…
- UniProt
- P01903, A0A0A1I7H6
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 46% strand | P01903 |
| B, E | MHC class II antigen | protein | 189 | 19% helix, 45% strand | A0A0A1I7H6 |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 15% helix, 47% strand | P01903 |
| C, F | VIMENTIN59-71 | protein | 13 | 0% helix, 8% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D, E
- EDO · 1,2-ethanediol · additive · 7 copies · chains B, C, E, F, D
- PGE · Triethylene glycol · additive · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.77 | 0.87 | 35 | EDO, PGE |
| 2 | 371 | 0.74 | 0.85 | 33 | PGE |
| 3 | 555 | 0.66 | 0.77 | 55 | empty |
| 4 | 570 | 0.66 | 0.76 | 48 | empty |
| 5 | 127 | 0.47 | 0.78 | 19 | empty |
Interfaces
10 interfaces between chains.
- D–E · 2458 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2450 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 770 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 725 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 720 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 6ATF · PDBe 6ATF · UniProt P01903 · UniProt A0A0A1I7H6
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