MolNFT v1 · #157119 · protein
Crystal structures of the murine class I major histocompatibility complex H-2DB in complex with the TRP1-M9 peptide
6MP0 · TRP1-M9 peptide, beta-2-MICROGLOBULIN,H-2 class I…: “Crystal structures of the murine class I major histocompatibility complex H-2DB in complex with the TRP1-M9…”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability…
- PDB
- 6MP0
- Type
- protein
- Length
- 388 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRP1-M9 peptide, beta-2-MICROGLOBULIN,H-2 class I histocompatibility antigen, D-B alpha…
- EC
- 1.14.18.-
- UniProt
- P07147, P01887, P01899
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRP1-M9 peptide, beta-2-MICROGLOBULIN,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct (EC 1.14.18.-) | protein | 388 | 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
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 | 622 | 0.67 | 0.76 | 53 | empty |
| 2 | 79 | 0.42 | 0.79 | 17 | empty |
| 3 | 72 | 0.36 | 0.77 | 15 | empty |
| 4 | 67 | 0.32 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MP0 · 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
- 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
- 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 0.24
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 6MP0 · PDBe 6MP0 · UniProt P07147 · UniProt P01887 · UniProt P01899
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