Research workbench
Crystal structure of NP1-B17 TCR-H2DB-np complex
Analyse Crystal structure of NP1-B17 TCR-H2DB-np complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SWZ
- Type
- protein
- Length
- 3,248 residues
- Chains
- 20
- 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; Influenza…
- UniProt
- P01899, P01887
- Ligands
- NA, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 12 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, K | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 277 | 28% helix, 38% strand | P01899 |
| B, G, L | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, H, M, R | Influenza NP366 epitope | protein | 9 | 0% helix, 0% strand | — |
| D | NP1-B17 TCR alpha chain | protein | 198 | 2% helix, 41% strand | — |
| E, J | NP1-B17 TCR beta chain | protein | 240 | 5% helix, 48% strand | — |
| I | NP1-B17 TCR alpha chain | protein | 186 | 2% helix, 40% strand | — |
| N | NP1-B17 TCR alpha chain | protein | 201 | 3% helix, 45% strand | — |
| O | NP1-B17 TCR beta chain | protein | 241 | 5% helix, 49% strand | — |
| P | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 238 | 30% helix, 31% strand | P01899 |
| Q | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| S | NP1-B17 TCR alpha chain | protein | 203 | 1% helix, 42% strand | — |
| T | NP1-B17 TCR beta chain | protein | 239 | 3% helix, 49% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains D, E, I, L, J, K, T, P
- SO4 · Sulfate ion · ion · 5 copies · chains D, A, E, K, O, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.80 | 0.82 | 114 | empty |
| 2 | 948 | 0.79 | 0.81 | 79 | empty |
| 3 | 1044 | 0.78 | 0.80 | 79 | empty |
| 4 | 1100 | 0.77 | 0.79 | 83 | empty |
| 5 | 830 | 0.73 | 0.78 | 79 | empty |
Interfaces
43 interfaces between chains.
- D–E · 2226 Ų buried · 17 hydrogen bonds · protein-protein
- N–O · 2210 Ų buried · 16 hydrogen bonds · protein-protein
- S–T · 2178 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 2123 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1371 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5SWZ · Crystal Structure of NP1-B17 TCR-H2Db-NP complex · the same entry in another collection · chain T against T, 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
- Every structure of UniProt P01899
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 5SWZ · PDBe 5SWZ · UniProt P01899 · UniProt P01887
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