Research workbench
The complex of GTF2B peptide tgaasfdef presented by H2-kd
Analyse The complex of GTF2B peptide tgaasfdef presented by H2-kd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D5E
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2-microglobulin…
- EC
- 2.3.1.48
- UniProt
- P01900, P01887, P62915
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 274 | 28% helix, 38% strand | P01900 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P01887 |
| P | Transcription initiation factor iib (EC 2.3.1.48) | protein | 9 | 0% helix, 0% strand | P62915 |
Ligands and binding sites
- GOL · Glycerol · additive · 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 | 544 | 0.65 | 0.77 | 48 | empty |
| 2 | 154 | 0.47 | 0.77 | 22 | empty |
| 3 | 57 | 0.35 | 0.78 | 16 | empty |
| 4 | 70 | 0.32 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1346 Ų buried · 24 hydrogen bonds · protein-protein
- A–P · 833 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 8D5E · The complex of Gtf2b Peptide TGAASFDEF Presented by H2-Dd · 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
- P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P62915 · AlphaFold monomer V2.0 prediction for transcription initiation factor iib (P62915) · a predicted model of the same protein · chain P against A, TM-score 0.44
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 P01900
- Every structure of UniProt P01887
- Every structure of UniProt P62915
- Elsewhere: RCSB PDB 8D5E · PDBe 8D5E · UniProt P01900 · UniProt P01887 · UniProt P62915
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