MolNFT v1 · #135748 · protein
Crystal structure of a cross-module fragment from the dimodular nrps dhbf
5U89 · Amino acid adenylation domain protein: “Crystal structure of a cross-module fragment from the dimodular nrps dhbf”. X-ray diffraction, 1 ligand (MJ8), 9 pockets (best druggability 0.85). MolNFT v1 #135748 on GenesisL1: 3D structure…
- PDB
- 5U89
- Type
- protein
- Length
- 1,103 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino acid adenylation domain protein; Mbth domain protein
- UniProt
- A0A0F6BHX2, A0A0F6BHX3
- Ligands
- MJ8
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amino acid adenylation domain protein | protein | 1039 | 36% helix, 23% strand | A0A0F6BHX2 |
| B | Mbth domain protein | protein | 64 | 17% helix, 30% strand | A0A0F6BHX3 |
Ligands and binding sites
- MJ8 · 5'-({[(2R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}propyl]sulfonyl}amino)-5'-deoxyadenosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.85 | 0.86 | 114 | empty |
| 2 | 1161 | 0.81 | 0.82 | 124 | MJ8 |
| 3 | 247 | 0.60 | 0.80 | 46 | empty |
| 4 | 118 | 0.56 | 0.83 | 32 | empty |
| 5 | 112 | 0.52 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5U89 · Crystal structure of a cross-module fragment from the dimodular NRPS DhbF · 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 A0A0F6BHX2
- Every structure of UniProt A0A0F6BHX3
- Elsewhere: RCSB PDB 5U89 · PDBe 5U89 · UniProt A0A0F6BHX2 · UniProt A0A0F6BHX3
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