Research workbench
Structure of the qdm peptide bound to qa-1A
Analyse Structure of the qdm peptide bound to qa-1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VCL
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H2-T23 protein; Beta-2-microglobulin; Qdm peptide
- UniProt
- Q31153, P01887, P01897
- Ligands
- NA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H2-T23 protein | protein | 277 | 27% helix, 39% strand | Q31153 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| P | Qdm peptide | protein | 9 | 0% helix, 0% strand | P01897 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, P
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.67 | 0.77 | 54 | GOL, NA |
| 2 | 132 | 0.41 | 0.75 | 26 | empty |
| 3 | 82 | 0.41 | 0.79 | 17 | empty |
| 4 | 62 | 0.40 | 0.80 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1282 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 896 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5VCL · Structure of the Qdm peptide bound to Qa-1a · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01897 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, L-D alpha… · a predicted model of the same protein · chain P against A, TM-score 0.29
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 Q31153
- Every structure of UniProt P01887
- Every structure of UniProt P01897
- Elsewhere: RCSB PDB 5VCL · PDBe 5VCL · UniProt Q31153 · UniProt P01887 · UniProt P01897
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