MolNFT v1 · #100995 · protein + DNA
Human MHF1-MHF2 DNA complex
4NDY · DNA (26-mer): “Human MHF1-MHF2 DNA complex”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #100995 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NDY
- Type
- protein + DNA
- Length
- 1,822 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (26-mer); Centromere protein S; Centromere protein X
- UniProt
- Q8N2Z9, A8MT69
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 79% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, O | DNA (26-mer) | dna | 26 | — | — |
| F, P | DNA (26-mer) | dna | 26 | — | — |
| C, G, A, J, R, S | Centromere protein S | protein | 93 | 84% helix, 2% strand | Q8N2Z9 |
| D, H, B, L, M, N, U, V, W, X | Centromere protein X | protein | 74 | 69% helix, 3% strand | A8MT69 |
| I, K, Q, T | Centromere protein S | protein | 105 | 82% helix, 4% strand | Q8N2Z9 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.75 | 0.87 | 30 | empty |
| 2 | 254 | 0.73 | 0.87 | 32 | empty |
| 3 | 794 | 0.67 | 0.74 | 83 | empty |
| 4 | 630 | 0.65 | 0.75 | 59 | empty |
| 5 | 239 | 0.64 | 0.82 | 28 | empty |
Interfaces
60 interfaces between chains.
- I–M · 2528 Ų buried · 18 hydrogen bonds · protein-protein
- Q–V · 2526 Ų buried · 19 hydrogen bonds · protein-protein
- R–W · 2524 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 2509 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 2503 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4NDY · Human MHF1-MHF2 DNA complex · 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 Q8N2Z9
- Every structure of UniProt A8MT69
- Elsewhere: RCSB PDB 4NDY · PDBe 4NDY · UniProt Q8N2Z9 · UniProt A8MT69
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