MolNFT v1 · #181119 · protein
Crystal structure of PHF1 tudor domain in complex with a peptidomimetic ligand UNC6641
7LKY · Isoform 1 of phd finger protein 1: “Crystal structure of PHF1 tudor domain in complex with a peptidomimetic ligand UNC6641”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.71). MolNFT v1 #181119 on GenesisL1: 3D…
- PDB
- 7LKY
- Type
- protein
- Length
- 501 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 1 of phd finger protein 1; Peptidomimetic inhibitor UNC6641
- UniProt
- O43189
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, H | Isoform 1 of phd finger protein 1 | protein | 56 | 5% helix, 52% strand | O43189 |
| B, C, F, G | Isoform 1 of phd finger protein 1 | protein | 55 | 5% helix, 51% strand | O43189 |
| J, I, K, L, M, N, O | Peptidomimetic inhibitor UNC6641 | protein | 7 | 0% helix, 14% strand | — |
| P | Peptidomimetic inhibitor UNC6641 | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, I, B, J, C, K, D, L, E, H, M, P
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains D, A, C, E, I, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.71 | 0.77 | 68 | empty |
| 2 | 875 | 0.71 | 0.76 | 79 | empty |
| 3 | 207 | 0.49 | 0.75 | 31 | DMS |
| 4 | 80 | 0.35 | 0.76 | 17 | DMS |
| 5 | 60 | 0.32 | 0.76 | 16 | empty |
Interfaces
35 interfaces between chains.
- H–P · 613 Ų buried · 7 hydrogen bonds · protein-protein
- C–K · 576 Ų buried · 6 hydrogen bonds · protein-protein
- G–O · 576 Ų buried · 5 hydrogen bonds · protein-protein
- F–N · 563 Ų buried · 6 hydrogen bonds · protein-protein
- E–M · 560 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 7LKY · Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 · the same entry in another collection · chain I against I, 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 O43189
- Elsewhere: RCSB PDB 7LKY · PDBe 7LKY · UniProt O43189
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