Research workbench
Crystal structure of H88A mutated human transthyretin
Analyse Crystal structure of H88A mutated human transthyretin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H0V
- Type
- protein
- Length
- 465 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02766
- Ligands
- MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Transthyretin | protein | 116 | 7% helix, 53% strand | P02766 |
| D | Transthyretin | protein | 117 | 6% helix, 50% strand | P02766 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.77 | 0.97 | 29 | MPD |
| 2 | 321 | 0.68 | 0.82 | 44 | empty |
| 3 | 300 | 0.66 | 0.82 | 37 | empty |
| 4 | 96 | 0.43 | 0.78 | 17 | empty |
| 5 | 97 | 0.38 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 916 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 884 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 429 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 348 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 332 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5H0V · Crystal structure of H88A mutated human transthyretin · 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 P02766
- Elsewhere: RCSB PDB 5H0V · PDBe 5H0V · UniProt P02766
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