Research workbench
Crystal structure of dhbe in complex with dhb and AMP
Analyse Crystal structure of dhbe in complex with dhb and AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MD9
- Type
- protein
- Length
- 536 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-dihydroxybenzoate-AMP ligase
- EC
- 6.3.2.-
- UniProt
- P40871
- Ligands
- AMP, DBH
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-dihydroxybenzoate-AMP ligase (EC 6.3.2.-) | protein | 536 | 34% helix, 26% strand | P40871 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- DBH · 2,3-dihydroxy-benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.83 | 0.86 | 91 | AMP, DBH |
| 2 | 86 | 0.47 | 0.81 | 24 | empty |
| 3 | 142 | 0.44 | 0.76 | 34 | empty |
| 4 | 83 | 0.30 | 0.73 | 21 | empty |
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
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 P40871
- Elsewhere: RCSB PDB 1MD9 · PDBe 1MD9 · UniProt P40871
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