Research workbench
42F3 P5E8/H2-ld complex
Analyse 42F3 P5E8/H2-ld complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TPU
- Type
- protein
- Length
- 2,510 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 42F3 alpha; 42F3 beta; H2-ld SBM2; P5E8 peptide
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 21% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 42F3 alpha | protein | 205 | 6% helix, 39% strand | — |
| B, D, H, N | 42F3 beta | protein | 240 | 8% helix, 53% strand | — |
| I | H2-ld SBM2 | protein | 173 | 39% helix, 31% strand | — |
| J, F, L, R | P5E8 peptide | protein | 9 | 0% helix, 0% strand | — |
| C, M | 42F3 alpha | protein | 204 | 4% helix, 40% strand | — |
| E | H2-ld SBM2 | protein | 175 | 38% helix, 31% strand | — |
| G | 42F3 alpha | protein | 202 | 6% helix, 41% strand | — |
| K | H2-ld SBM2 | protein | 175 | 38% helix, 31% strand | — |
| Q | H2-ld SBM2 | protein | 176 | 39% helix, 31% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, E, G, H, K, N, Q
- EDO · 1,2-ethanediol · additive · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.84 | 0.85 | 119 | empty |
| 2 | 1050 | 0.75 | 0.78 | 85 | empty |
| 3 | 1019 | 0.74 | 0.77 | 78 | empty |
| 4 | 699 | 0.73 | 0.80 | 83 | empty |
| 5 | 664 | 0.73 | 0.80 | 70 | empty |
Interfaces
35 interfaces between chains.
- C–D · 2122 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2117 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2063 Ų buried · 26 hydrogen bonds · protein-protein
- M–N · 2057 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 987 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 3TPU · 42F3 p5E8/H2-Ld complex · the same entry in another collection · chain A against A, 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 3TPU · PDBe 3TPU
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