Research workbench
H2-ld complexed with A5 peptide
Analyse H2-ld complexed with A5 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L9N
- Type
- protein
- Length
- 1,544 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC; B2M; Ser-pro-ser-tyr-ala-tyr-his-gln-phe
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | MHC | protein | 278 | 27% helix, 40% strand | — |
| B, E, H, K | B2M | protein | 99 | 0% helix, 49% strand | — |
| C, F, I, L | Ser-pro-ser-tyr-ala-tyr-his-gln-phe | protein | 9 | 0% helix, 0% strand | — |
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.83 | 0.84 | 94 | empty |
| 2 | 1050 | 0.81 | 0.83 | 84 | empty |
| 3 | 1119 | 0.81 | 0.83 | 95 | empty |
| 4 | 1085 | 0.81 | 0.82 | 90 | empty |
| 5 | 175 | 0.57 | 0.81 | 30 | empty |
Interfaces
16 interfaces between chains.
- D–E · 1251 Ų buried · 21 hydrogen bonds · protein-protein
- J–K · 1250 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1250 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1247 Ų buried · 19 hydrogen bonds · protein-protein
- G–J · 1105 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6L9N · H2-Ld complexed with A5 peptide · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6L9N · PDBe 6L9N
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