Research workbench
Crystal structure of helicobacter pylori pseudaminic acid biosynthesis N -acetyltransferase pseh complex with acetyl-CoA
Analyse Crystal structure of helicobacter pylori pseudaminic acid biosynthesis N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RI1
- Type
- protein
- Length
- 532 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N- acetyltransferase
- EC
- 2.3.1.202
- UniProt
- O25094
- Ligands
- ACO
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N- acetyltransferase (EC 2.3.1.202) | protein | 178 | 35% helix, 37% strand | O25094 |
| B | Udp-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N- acetyltransferase (EC 2.3.1.202) | protein | 179 | 37% helix, 36% strand | O25094 |
| C | Udp-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N- acetyltransferase (EC 2.3.1.202) | protein | 175 | 35% helix, 37% strand | O25094 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.83 | 0.84 | 93 | ACO, ACT |
| 2 | 564 | 0.74 | 0.81 | 43 | ACO, ACT |
| 3 | 163 | 0.67 | 0.87 | 23 | empty |
| 4 | 179 | 0.45 | 0.74 | 20 | empty |
| 5 | 144 | 0.42 | 0.75 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1023 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 647 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4RI1 · Crystal structure of Helicobacter pylori pseudaminic acid biosynthesis N… · the same entry in another collection · chain A against A, TM-score 1.00
- O25094 · AlphaFold monomer V2.0 prediction for udp-4-amino-4,6-dideoxy-N… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O25094
- Elsewhere: RCSB PDB 4RI1 · PDBe 4RI1 · UniProt O25094
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