MolNFT v1 · #94313 · protein + DNA
Molecular basis of vancomycin resistance transfer in staphylococcus aureus
4HT4 · Nicking enzyme: “Molecular basis of vancomycin resistance transfer in staphylococcus aureus”. X-ray diffraction, 3 ligands (CA, NI, CL), 3 pockets (best druggability 0.48). MolNFT v1 #94313 on GenesisL1: 3D structure, binding sites…
- PDB
- 4HT4
- Type
- protein + DNA
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicking enzyme; DNA (28-mer)
- UniProt
- Q53632
- Ligands
- CA, NI, CL
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicking enzyme | protein | 194 | 31% helix, 25% strand | Q53632 |
| B | DNA (28-mer) | dna | 28 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.48 | 0.75 | 33 | NI, CA, CL |
| 2 | 52 | 0.40 | 0.82 | 11 | empty |
| 3 | 58 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1627 Ų buried · 50 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 4HT4 · Molecular Basis of Vancomycin Resistance Transfer in Staphylococcus aureus · 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 Q53632
- Elsewhere: RCSB PDB 4HT4 · PDBe 4HT4 · UniProt Q53632
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