Research workbench
Structure of base N-terminal domain from acinetobacter baumannii bound to 6-(P-BENZYLOXY)PHENYL-1-(pyridin-4-ylmethyl)-1H-PYRAZOLO[3,4- B]PYRIDINE-4-carboxylic acid.
Analyse Structure of base N-terminal domain from acinetobacter baumannii bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U16
- Type
- protein
- Length
- 870 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide arylation enzyme
- EC
- 6.2.1.-
- UniProt
- B2HVG8
- Ligands
- H89, CA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide arylation enzyme (EC 6.2.1.-) | protein | 433 | 35% helix, 23% strand | B2HVG8 |
| B | Peptide arylation enzyme (EC 6.2.1.-) | protein | 437 | 35% helix, 22% strand | B2HVG8 |
Ligands and binding sites
- H89 · 6-[4-(benzyloxy)phenyl]-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.77 | 0.79 | 118 | H89, CA |
| 2 | 280 | 0.63 | 0.81 | 34 | empty |
| 3 | 95 | 0.47 | 0.81 | 24 | empty |
| 4 | 204 | 0.46 | 0.74 | 30 | empty |
| 5 | 102 | 0.41 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3U16 · Structure of BasE N-terminal domain from Acinetobacter baumannii 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 B2HVG8
- Elsewhere: RCSB PDB 3U16 · PDBe 3U16 · UniProt B2HVG8
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