Research workbench
Crystal structure of murine class I H-2DB complexed with peptide GP33 (C9M/K1S)
Analyse Crystal structure of murine class I H-2DB complexed with peptide GP33 (C9M/K1S) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FFP
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B, alpha chain; Beta-2 microglobulin beta…
- UniProt
- P01899, P01887
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, D-B, alpha chain | protein | 273 | 28% helix, 38% strand | P01899 |
| B, E | Beta-2 microglobulin beta chain | protein | 100 | 0% helix, 49% strand | P01887 |
| C, F | Synthetic peptide with sequence ser-ala-val-tyr- asn-phe-ala-thr-met | protein | 9 | 0% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.64 | 0.75 | 50 | empty |
| 2 | 544 | 0.63 | 0.75 | 47 | empty |
| 3 | 78 | 0.40 | 0.78 | 25 | empty |
| 4 | 57 | 0.40 | 0.81 | 18 | empty |
| 5 | 58 | 0.31 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1393 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1380 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 904 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 893 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1FFP · Crystal structure of murine class I H-2DB complexed with peptide GP33 (C9M/K1S) · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P01899
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 1FFP · PDBe 1FFP · UniProt P01899 · UniProt P01887
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