Research workbench
Crystal structure of phosphopantetheine adenylyltransferase (TM0741) from thermotoga maritima at 2.20 a resolution
Analyse Crystal structure of phosphopantetheine adenylyltransferase (TM0741) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VLH
- Type
- protein
- Length
- 945 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- Q9WZK0
- Ligands
- PNS
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 42% helix, 20% strand | Q9WZK0 |
| B, C, D | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 158 | 41% helix, 20% strand | Q9WZK0 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 6 copies · chains A, E, B, F, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.83 | 0.85 | 93 | PNS |
| 2 | 419 | 0.81 | 0.89 | 60 | PNS |
| 3 | 418 | 0.81 | 0.89 | 51 | PNS |
| 4 | 403 | 0.81 | 0.89 | 55 | PNS |
| 5 | 354 | 0.81 | 0.90 | 49 | PNS |
Interfaces
13 interfaces between chains.
- A–B · 1051 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1014 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1001 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 661 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 652 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1VLH · Crystal structure of Phosphopantetheine adenylyltransferase (TM0741) from Thermotoga… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9WZK0 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (Q9WZK0) · a predicted model of the same protein · chain C 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 Q9WZK0
- Elsewhere: RCSB PDB 1VLH · PDBe 1VLH · UniProt Q9WZK0
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