MolNFT v1 · #72905 · protein + DNA
HMGD(M13A)-DNA complex
3NM9 · High mobility group protein D: “HMGD(M13A)-DNA complex”. X-ray diffraction, 7 pockets (best druggability 0.79). MolNFT v1 #72905 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NM9
- Type
- protein + DNA
- Length
- 539 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High mobility group protein D; DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
- UniProt
- Q05783
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P | High mobility group protein D | protein | 73 | 73% helix, 0% strand | Q05783 |
| B, C, E, F, H, I, K, N, O | DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' | dna | 10 | — | — |
| L | DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' | dna | 11 | — | — |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.79 | 0.82 | 65 | empty |
| 2 | 843 | 0.78 | 0.81 | 81 | empty |
| 3 | 249 | 0.74 | 0.88 | 33 | empty |
| 4 | 281 | 0.67 | 0.83 | 50 | empty |
| 5 | 140 | 0.51 | 0.80 | 20 | empty |
Interfaces
41 interfaces between chains.
- N–O · 457 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- E–F · 456 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- B–C · 447 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- H–I · 442 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- K–L · 441 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Compared structures
- 3NM9 · HMGD(M13A)-DNA complex · the same entry in another collection · chain O against O, 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 Q05783
- Elsewhere: RCSB PDB 3NM9 · PDBe 3NM9 · UniProt Q05783
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