Research workbench
T1L reovirus SIGMA1 complexed with 5C6 Fab fragments
Analyse T1L reovirus SIGMA1 complexed with 5C6 Fab fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MHS
- Type
- protein
- Length
- 1,736 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein sigma-1; 5C6 Fab light chain; 5C6 Fab heavy chain
- UniProt
- P04506
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer capsid protein sigma-1 | protein | 163 | 5% helix, 61% strand | P04506 |
| D | 5C6 Fab light chain | protein | 214 | 5% helix, 49% strand | — |
| E | 5C6 Fab heavy chain | protein | 210 | 3% helix, 51% strand | — |
| F | 5C6 Fab light chain | protein | 212 | 5% helix, 45% strand | — |
| G | 5C6 Fab light chain | protein | 205 | 5% helix, 46% strand | — |
| H | 5C6 Fab heavy chain | protein | 201 | 3% helix, 44% strand | — |
| N | 5C6 Fab heavy chain | protein | 205 | 4% helix, 47% strand | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.86 | 0.97 | 33 | empty |
| 2 | 587 | 0.73 | 0.81 | 77 | empty |
| 3 | 350 | 0.70 | 0.83 | 51 | empty |
| 4 | 710 | 0.69 | 0.77 | 101 | empty |
| 5 | 76 | 0.66 | 0.93 | 23 | empty |
Interfaces
16 interfaces between chains.
- D–E · 1368 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1236 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 1218 Ų buried · 5 hydrogen bonds · protein-protein
- G–N · 1140 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1135 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5MHS · T1L reovirus sigma1 complexed with 5C6 Fab fragments · the same entry in another collection · chain F against F, 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 P04506
- Elsewhere: RCSB PDB 5MHS · PDBe 5MHS · UniProt P04506
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