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Crystal structure of inorganic pyrophosphatase from legionella pneumophila philadelphia 1
Analyse Crystal structure of inorganic pyrophosphatase from legionella pneumophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N1C
- Type
- protein
- Length
- 1,029 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q5ZRW2
- Ligands
- ALA, NA
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 175 | 22% helix, 33% strand | Q5ZRW2 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 171 | 20% helix, 35% strand | Q5ZRW2 |
| C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 167 | 22% helix, 34% strand | Q5ZRW2 |
| D, F | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 171 | 21% helix, 34% strand | Q5ZRW2 |
| E | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 174 | 21% helix, 36% strand | Q5ZRW2 |
Ligands and binding sites
- ALA · Alanine · ligand · 2 copies · chains A, B, D, C, E, F
- NA · Sodium ion · metal · 4 copies · chains A, F, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B, D, F, C, E
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.82 | 0.84 | 71 | MPD, ALA |
| 2 | 778 | 0.81 | 0.84 | 64 | MPD, ALA |
| 3 | 718 | 0.81 | 0.84 | 63 | MPD |
| 4 | 685 | 0.75 | 0.81 | 79 | empty |
| 5 | 538 | 0.71 | 0.80 | 65 | empty |
Interfaces
12 interfaces between chains.
- A–B · 650 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 641 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 639 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 559 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 549 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6N1C · Crystal structure of Inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1 · 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 Q5ZRW2
- Elsewhere: RCSB PDB 6N1C · PDBe 6N1C · UniProt Q5ZRW2
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