MolNFT v1 · #139436 · protein + DNA
Binary complex of PHF1 and a double stranded DNA
5XFP · Phd finger protein 1: “Binary complex of PHF1 and a double stranded DNA”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.69). MolNFT v1 #139436 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XFP
- Type
- protein + DNA
- Length
- 937 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 1; DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
- UniProt
- O43189
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein 1 | protein | 306 | 27% helix, 21% strand | O43189 |
| B | Phd finger protein 1 | protein | 305 | 28% helix, 20% strand | O43189 |
| C, D | DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3') | dna | 13 | — | — |
| E | Phd finger protein 1 | protein | 300 | 28% helix, 21% strand | O43189 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.69 | 0.80 | 51 | empty |
| 2 | 503 | 0.68 | 0.78 | 53 | empty |
| 3 | 386 | 0.64 | 0.78 | 42 | empty |
| 4 | 594 | 0.63 | 0.74 | 57 | empty |
| 5 | 56 | 0.36 | 0.79 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 604 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–B · 469 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 262 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–E · 172 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 5XFP · PDBe 5XFP · UniProt O43189
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