MolNFT v1 · #136973 · protein + DNA
Structure of mycobacterium smegmatis helicase lhr bound to ssdna and AMP-pnp
5V9X · ATP-dependent DNA helicase: “Structure of mycobacterium smegmatis helicase lhr bound to ssdna and AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 13 pockets (best druggability 0.89). MolNFT v1 #136973 on GenesisL1: 3D structure…
- PDB
- 5V9X
- Type
- protein + DNA
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase; Ssdna
- EC
- 3.6.4.13
- UniProt
- A0A0D6HFY2
- Ligands
- ANP, MG
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase (EC 3.6.4.13) | protein | 772 | 47% helix, 14% strand | A0A0D6HFY2 |
| B | Ssdna | dna | 13 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.89 | 0.91 | 97 | PEG |
| 2 | 127 | 0.73 | 0.93 | 25 | empty |
| 3 | 136 | 0.69 | 0.90 | 23 | empty |
| 4 | 264 | 0.68 | 0.84 | 36 | ANP, GOL, MG |
| 5 | 121 | 0.53 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1817 Ų buried · 40 hydrogen bonds · protein-nucleic
Compared structures
- 5V9X · Structure of Mycobacterium smegmatis helicase Lhr bound to ssDNA and AMP-PNP · the same entry in another collection · chain A against A, 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 A0A0D6HFY2
- Elsewhere: RCSB PDB 5V9X · PDBe 5V9X · UniProt A0A0D6HFY2
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