MolNFT v1 · #124894 · protein
Crystal structure of HLA-DQ2.5-CLIP2
5KSV · MHC class II HLA-dq-alpha chain: “Crystal structure of HLA-DQ2.5-CLIP2”. X-ray diffraction, 3 pockets (best druggability 0.54). MolNFT v1 #124894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KSV
- Type
- protein
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; MHC class II HLA-dq-beta-1; HLA class II…
- UniProt
- O19705, O19712
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 180 | 14% helix, 44% strand | O19705 |
| B | MHC class II HLA-dq-beta-1 | protein | 180 | 22% helix, 46% strand | O19712 |
| C | HLA class II histocompatibility antigen gamma chain | protein | 12 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.54 | 0.74 | 53 | empty |
| 2 | 72 | 0.30 | 0.73 | 20 | empty |
| 3 | 61 | 0.29 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2617 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 715 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 581 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5KSV · Crystal structure of HLA-DQ2.5-CLIP2 · the same entry in another collection · chain A against A, TM-score 1.00
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 O19705
- Every structure of UniProt O19712
- Elsewhere: RCSB PDB 5KSV · PDBe 5KSV · UniProt O19705 · UniProt O19712
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