Research workbench
42F3 QL9/H2-ld complex
Analyse 42F3 QL9/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
- 3TF7
- Type
- protein
- Length
- 1,272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H2-ld SBM2; QL9 peptide (qlspfpfdl); 42F3 MUT7 scfv (42F3 alpha chain, linker, 42F3 beta…
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | H2-ld SBM2 | protein | 175 | 38% helix, 35% strand | — |
| F, B | QL9 peptide (qlspfpfdl) | protein | 9 | 0% helix, 0% strand | — |
| C | 42F3 MUT7 scfv (42F3 alpha chain, linker, 42F3 beta chain) | protein | 232 | 4% helix, 50% strand | — |
| A | H2-ld SBM2 | protein | 175 | 37% helix, 31% strand | — |
| G | 42F3 MUT7 scfv (42F3 alpha chain, linker, 42F3 beta chain) | protein | 224 | 4% helix, 52% strand | — |
| I | 42F3 MUT7 scfv (42F3 alpha chain, linker, 42F3 beta chain) | protein | 228 | 4% helix, 49% strand | — |
| K | 42F3 MUT7 scfv (42F3 alpha chain, linker, 42F3 beta chain) | protein | 220 | 1% helix, 47% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains C, A, B, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.73 | 0.79 | 72 | empty |
| 2 | 625 | 0.71 | 0.79 | 57 | empty |
| 3 | 543 | 0.68 | 0.78 | 53 | empty |
| 4 | 356 | 0.65 | 0.80 | 33 | empty |
| 5 | 279 | 0.60 | 0.79 | 38 | GOL |
Interfaces
11 interfaces between chains.
- A–B · 960 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 960 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 763 Ų buried · 8 hydrogen bonds · protein-protein
- C–K · 698 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 684 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3TF7 · 42F3 QL9/H2-Ld complex · the same entry in another collection · chain E against E, 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 3TF7 · PDBe 3TF7
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