Research workbench
T3D reovirus SIGMA1 complexed with 9BG5 Fab fragments
Analyse T3D reovirus SIGMA1 complexed with 9BG5 Fab fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MHR
- Type
- protein
- Length
- 3,120 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viral attachment protein sigma 1; 9BG5 Fab light CHAIN,LOC100046793 PROTEIN,MAB 110 light…
- UniProt
- Q86335
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 15 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Viral attachment protein sigma 1 | protein | 162 | 5% helix, 57% strand | Q86335 |
| B, D, F | Viral attachment protein sigma 1 | protein | 163 | 5% helix, 58% strand | Q86335 |
| C | Viral attachment protein sigma 1 | protein | 162 | 5% helix, 57% strand | Q86335 |
| G | 9BG5 Fab light CHAIN,LOC100046793 PROTEIN,MAB 110 light chain | protein | 211 | 7% helix, 54% strand | — |
| H | 9BG5 Fab light CHAIN,LOC100046793 PROTEIN,MAB 110 light chain | protein | 205 | 5% helix, 48% strand | — |
| I | 9BG5 Fab heavy chain | protein | 213 | 5% helix, 53% strand | — |
| J | 9BG5 Fab light CHAIN,LOC100046793 PROTEIN,MAB 110 light chain | protein | 108 | 6% helix, 49% strand | — |
| K | 9BG5 Fab heavy chain | protein | 122 | 5% helix, 50% strand | — |
| L | 9BG5 Fab light CHAIN,LOC100046793 PROTEIN,MAB 110 light chain | protein | 107 | 6% helix, 48% strand | — |
| M | 9BG5 Fab heavy chain | protein | 119 | 3% helix, 47% strand | — |
| N | 9BG5 Fab heavy chain | protein | 214 | 5% helix, 52% strand | — |
| O | 9BG5 Fab light CHAIN,LOC100046793 PROTEIN,MAB 110 light chain | protein | 210 | 8% helix, 50% strand | — |
| P | 9BG5 Fab heavy chain | protein | 213 | 3% helix, 51% strand | — |
| Q | 9BG5 Fab light CHAIN,LOC100046793 PROTEIN,MAB 110 light chain | protein | 210 | 7% helix, 49% strand | — |
| R | 9BG5 Fab heavy chain | protein | 213 | 5% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.87 | 0.94 | 37 | empty |
| 2 | 431 | 0.86 | 0.94 | 36 | empty |
| 3 | 547 | 0.70 | 0.79 | 62 | empty |
| 4 | 603 | 0.70 | 0.78 | 60 | empty |
| 5 | 547 | 0.69 | 0.79 | 61 | empty |
Interfaces
41 interfaces between chains.
- O–P · 1708 Ų buried · 15 hydrogen bonds · protein-protein
- G–N · 1636 Ų buried · 15 hydrogen bonds · protein-protein
- Q–R · 1570 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 1559 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1242 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5MHR · T3D reovirus sigma1 complexed with 9BG5 Fab fragments · 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
- Every structure of UniProt Q86335
- Elsewhere: RCSB PDB 5MHR · PDBe 5MHR · UniProt Q86335
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