Research workbench
Crystal structure of an inorganic pyrophosphatase from chlamydia trachomatis D/UW-3/CX
Analyse Crystal structure of an inorganic pyrophosphatase from chlamydia trachomatis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WE5
- Type
- protein
- Length
- 618 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- O84777
- Ligands
- NA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 206 | 24% helix, 29% strand | O84777 |
| C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 206 | 24% helix, 29% strand | O84777 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.65 | 0.92 | 24 | empty |
| 2 | 228 | 0.61 | 0.81 | 38 | empty |
| 3 | 208 | 0.59 | 0.81 | 31 | empty |
| 4 | 189 | 0.53 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1125 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1122 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1021 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6WE5 · Crystal structure of an inorganic pyrophosphatase from Chlamydia trachomatis D/UW-3/Cx · the same entry in another collection · chain A against A, TM-score 1.00
- O84777 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (O84777) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O84777
- Elsewhere: RCSB PDB 6WE5 · PDBe 6WE5 · UniProt O84777
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