Research workbench
Crystal structures of the murine class I major histocompatibility complex H-2DB in complex with the mutant TRP1-K8 peptide
Analyse Crystal structures of the murine class I major histocompatibility complex H-2DB… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MP1
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRP1-K8 peptide, beta-2-MICROGLOBULIN,H-2 class I histocompatibility antigen, D-B alpha…
- EC
- 1.14.18.-
- UniProt
- P07147, P01887, P01899
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRP1-K8 peptide, beta-2-MICROGLOBULIN,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct (EC 1.14.18.-) | protein | 385 | 19% helix, 42% strand | P07147, P01887, P01899 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.68 | 0.78 | 54 | empty |
| 2 | 154 | 0.51 | 0.79 | 25 | empty |
| 3 | 111 | 0.48 | 0.80 | 22 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MP1 · Crystal structures of the murine class I major histocompatibility complex H-2Db in… · the same entry in another collection · chain A against A, TM-score 1.00
- P07147 · AlphaFold monomer V2.0 prediction for 5,6-dihydroxyindole-2-carboxylic acid oxidase… · a predicted model of the same protein · chain A against A, TM-score 0.26
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain A against A, TM-score 0.25
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 P07147
- Every structure of UniProt P01887
- Every structure of UniProt P01899
- Elsewhere: RCSB PDB 6MP1 · PDBe 6MP1 · UniProt P07147 · UniProt P01887 · UniProt P01899
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