MolNFT v1 · #112838 · protein
Crystal structure of holo-AB3403 a four domain nonribosomal peptide synthetase bound to AMP and glycine
4ZXI · Tyrocidine synthetase 3: “Crystal structure of holo-AB3403 a four domain nonribosomal peptide synthetase bound to AMP and glycine”. X-ray diffraction, 6 ligands (PNS, GLY, AMP), 14 pockets (best druggability 0.87). MolNFT v1 #112838…
- PDB
- 4ZXI
- Type
- protein
- Length
- 1,314 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrocidine synthetase 3
- UniProt
- B7H2D0
- Ligands
- PNS, GLY, AMP, XP4, NI, MG
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrocidine synthetase 3 | protein | 1314 | 36% helix, 21% strand | B7H2D0 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · chains A
- GLY · Glycine · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
- XP4 · 1,2-dimyristoyl-sn-glycero-3-phosphate · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.87 | 0.88 | 127 | PNS |
| 2 | 525 | 0.82 | 0.87 | 42 | XP4 |
| 3 | 1077 | 0.81 | 0.82 | 110 | GLY, AMP, MG |
| 4 | 477 | 0.76 | 0.84 | 65 | empty |
| 5 | 273 | 0.65 | 0.82 | 38 | empty |
Modifications
Observed in the structure: 1 cofactor (phosphopantetheinylation).
Compared structures
- 4ZXI · Crystal Structure of holo-AB3403 a four domain nonribosomal peptide synthetase bound to… · 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 B7H2D0
- Elsewhere: RCSB PDB 4ZXI · PDBe 4ZXI · UniProt B7H2D0
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