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Crystal structure of whirlin PDZ3_C-ter in complex with harmonin A1 C- terminal PDZ binding motif peptide
Analyse Crystal structure of whirlin PDZ3_C-ter in complex with harmonin A1 C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y9P
- Type
- protein
- Length
- 583 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Whirlin; Harmonin A1
- UniProt
- Q80VW5, Q6PPF3
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 8 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Whirlin | protein | 93 | 19% helix, 32% strand | Q80VW5 |
| B | Whirlin | protein | 90 | 20% helix, 32% strand | Q80VW5 |
| C | Harmonin A1 | protein | 8 | 0% helix, 25% strand | Q6PPF3 |
| D | Harmonin A1 | protein | 7 | 0% helix, 43% strand | Q6PPF3 |
| E | Whirlin | protein | 89 | 15% helix, 33% strand | Q80VW5 |
| F, J, L | Harmonin A1 | protein | 5 | 0% helix, 60% strand | Q6PPF3 |
| G, I, K | Whirlin | protein | 90 | 14% helix, 32% strand | Q80VW5 |
| H | Harmonin A1 | protein | 11 | 0% helix, 27% strand | Q6PPF3 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.71 | 0.77 | 76 | empty |
| 2 | 491 | 0.63 | 0.76 | 55 | empty |
| 3 | 107 | 0.55 | 0.84 | 23 | empty |
| 4 | 87 | 0.52 | 0.84 | 20 | empty |
| 5 | 168 | 0.51 | 0.78 | 27 | empty |
Interfaces
20 interfaces between chains.
- G–H · 484 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 412 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 402 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6Y9P · Crystal structure of Whirlin PDZ3_C-ter in complex with Harmonin a1 C-terminal PDZ… · the same entry in another collection · chain L against L, 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 Q80VW5
- Every structure of UniProt Q6PPF3
- Elsewhere: RCSB PDB 6Y9P · PDBe 6Y9P · UniProt Q80VW5 · UniProt Q6PPF3
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