MolNFT v1 · #102923 · protein + DNA
Crystal structure of human MUS81-EME1 in complex with 5'-flap DNA, and MG2+
4P0P · Crossover junction endonuclease MUS81: “Crystal structure of human MUS81-EME1 in complex with 5'-flap DNA, and MG2+”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.77). MolNFT v1 #102923 on GenesisL1: 3D…
- PDB
- 4P0P
- Type
- protein + DNA
- Length
- 594 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crossover junction endonuclease MUS81; Crossover junction endonuclease EME1; DNA…
- EC
- 3.1.22.-
- UniProt
- Q96NY9, Q96AY2
- Ligands
- MG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Crossover junction endonuclease MUS81 (EC 3.1.22.-) | protein | 283 | 39% helix, 20% strand | Q96NY9 |
| B | Crossover junction endonuclease EME1 (EC 3.1.22.-) | protein | 278 | 46% helix, 14% strand | Q96AY2 |
| E | DNA gaatgtgtgtctcaatc | dna | 16 | — | — |
| F | DNA ggattg | dna | 6 | — | — |
| G | DNA taaccagacacacatt | dna | 11 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.77 | 0.79 | 68 | empty |
| 2 | 352 | 0.73 | 0.84 | 47 | empty |
| 3 | 321 | 0.69 | 0.83 | 30 | empty |
| 4 | 285 | 0.54 | 0.76 | 32 | empty |
| 5 | 172 | 0.54 | 0.79 | 29 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3487 Ų buried · 45 hydrogen bonds · protein-protein
- E–G · 511 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–E · 470 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–G · 339 Ų buried · 4 hydrogen bonds · protein-nucleic
- E–F · 270 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Compared structures
- 4P0P · Crystal structure of Human Mus81-Eme1 in complex with 5'-flap DNA, and Mg2+ · the same entry in another collection · chain B against B, TM-score 1.00
- Q96NY9 · AlphaFold monomer V2.0 prediction for crossover junction endonuclease MUS81 (Q96NY9) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q96AY2 · AlphaFold monomer V2.0 prediction for crossover junction endonuclease EME1 (Q96AY2) · a predicted model of the same protein · chain B against A, TM-score 0.77
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 Q96NY9
- Every structure of UniProt Q96AY2
- Elsewhere: RCSB PDB 4P0P · PDBe 4P0P · UniProt Q96NY9 · UniProt Q96AY2
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