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A circular permutant of the tobacco mosaic virus (tmv) mutant Q101H coordinated with heme
Analyse A circular permutant of the tobacco mosaic virus (tmv) mutant Q101H coordinated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X0Q
- Type
- protein
- Length
- 2,380 residues
- Chains
- 17
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein circular permutant
- UniProt
- P69687
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q | Capsid protein circular permutant | protein | 140 | 50% helix, 10% strand | P69687 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 9 copies · chains C, D, G, J, K, L, N, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.28 | 0.73 | 18 | empty |
| 2 | 70 | 0.27 | 0.72 | 16 | empty |
| 3 | 66 | 0.27 | 0.72 | 16 | empty |
| 4 | 62 | 0.26 | 0.72 | 18 | empty |
| 5 | 56 | 0.25 | 0.73 | 16 | empty |
Interfaces
17 interfaces between chains.
- E–I · 1083 Ų buried · 15 hydrogen bonds · protein-protein
- H–O · 1077 Ų buried · 16 hydrogen bonds · protein-protein
- D–Q · 1073 Ų buried · 15 hydrogen bonds · protein-protein
- M–P · 1068 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1066 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6X0Q · A Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H coordinated with heme · the same entry in another collection · chain O against O, 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 P69687
- Elsewhere: RCSB PDB 6X0Q · PDBe 6X0Q · UniProt P69687
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