Research workbench
Decamer-like conformation of a nano-peptide bound to HLA- B3501 due to nonstandard positioning of the C-terminus
Analyse Decamer-like conformation of a nano-peptide bound to HLA- B3501 due to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A9B
- Type
- protein
- Length
- 772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-35 B*3501 (alpha chain); Beta-2-microglobulin…
- UniProt
- P30685, P61769
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B-35 B*3501 (alpha chain) | protein | 277 | 27% helix, 41% strand | P30685 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C, F | Peptide lpplditpy | protein | 9 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.75 | 0.78 | 69 | empty |
| 2 | 491 | 0.67 | 0.78 | 46 | empty |
| 3 | 512 | 0.66 | 0.77 | 56 | empty |
| 4 | 127 | 0.47 | 0.78 | 18 | empty |
| 5 | 141 | 0.46 | 0.77 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1433 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1431 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 852 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 852 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1A9B · Decamer-like conformation of a nano-peptide bound to HLA-B3501 due to nonstandard… · the same entry in another collection · chain C against C, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B 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 P30685
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1A9B · PDBe 1A9B · UniProt P30685 · UniProt P61769
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