MolNFT v1 · #158190 · protein
Ternary complex structure of the T130K mutant of ant-4 with neomycin, ampcpp and pyrophosphate
6NMM · Kanamycin nucleotidyltransferase: “Ternary complex structure of the T130K mutant of ant-4 with neomycin, ampcpp and pyrophosphate”. X-ray diffraction, 4 ligands (NMY, A, PPV), 10 pockets (best druggability 0.79). MolNFT v1 #158190…
- PDB
- 6NMM
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kanamycin nucleotidyltransferase
- UniProt
- Q57514
- Ligands
- NMY, A, PPV, MG
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Kanamycin nucleotidyltransferase | protein | 252 | 57% helix, 14% strand | Q57514 |
Ligands and binding sites
- NMY · Neomycin · ligand · 6 copies · chains A, D, B, C
- A · Adenosine-5'-monophosphate · ligand · 6 copies · chains A, D, B, C
- PPV · Pyrophosphate · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.79 | 0.80 | 116 | A, PPV, MG, NMY |
| 2 | 1197 | 0.78 | 0.80 | 128 | NMY, A, PPV, MG |
| 3 | 880 | 0.70 | 0.76 | 71 | empty |
| 4 | 216 | 0.59 | 0.81 | 35 | empty |
| 5 | 141 | 0.57 | 0.82 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2972 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2943 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 330 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 181 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6NMM · Ternary complex structure of the T130K mutant of ANT-4 with Neomycin, AMPCPP and… · 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 Q57514
- Elsewhere: RCSB PDB 6NMM · PDBe 6NMM · UniProt Q57514
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