MolNFT v1 · #52160 · protein
Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1
2VSP: “Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1”. X-ray diffraction, 6 pockets (best druggability 0.63). MolNFT v1 #52160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VSP
- Type
- protein
- Length
- 329 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PDZ domain-containing protein 1
- UniProt
- Q5T2W1
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | PDZ domain-containing protein 1 | protein | 83 | 14% helix, 30% strand | Q5T2W1 |
| B | PDZ domain-containing protein 1 | protein | 80 | 16% helix, 34% strand | Q5T2W1 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.63 | 0.81 | 43 | empty |
| 2 | 202 | 0.52 | 0.77 | 25 | empty |
| 3 | 116 | 0.51 | 0.81 | 21 | empty |
| 4 | 151 | 0.50 | 0.79 | 22 | empty |
| 5 | 150 | 0.48 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–D · 371 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 367 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 295 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 196 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 192 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VSP · Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5T2W1 · AlphaFold monomer V2.0 prediction for NA(+)/H(+) exchange regulatory cofactor nhe-RF3… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q5T2W1
- Elsewhere: RCSB PDB 2VSP · PDBe 2VSP · UniProt Q5T2W1
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