MolNFT v1 · #84053 · protein
Crystal structure of phosphoapantetheine adenylyltransferase PPAT/COAD with AMP-pnp from pseudomonas aerugonosa
3X1K · Phosphopantetheine adenylyltransferase: “Crystal structure of phosphoapantetheine adenylyltransferase PPAT/COAD with AMP-pnp from pseudomonas…”. X-ray diffraction, 2 ligands (ANP, PO4), 15 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 3X1K
- Type
- protein
- Length
- 944 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- A3LHH1
- Ligands
- ANP, PO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 46% helix, 18% strand | A3LHH1 |
| D, F | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 158 | 44% helix, 18% strand | A3LHH1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, C, B
- DMS · Dimethyl sulfoxide · additive · 16 copies · chains A, C, B, D, E, F
- FMT · Formic acid · additive · 6 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.82 | 0.86 | 78 | ANP, DMS, PO4 |
| 2 | 619 | 0.81 | 0.86 | 70 | ANP, GOL, DMS |
| 3 | 739 | 0.81 | 0.85 | 79 | DMS, ANP |
| 4 | 469 | 0.78 | 0.85 | 47 | ANP |
| 5 | 768 | 0.76 | 0.80 | 65 | FMT, ANP, DMS |
Interfaces
14 interfaces between chains.
- B–D · 1155 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1142 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1107 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 672 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3X1K · crystal structure of Phosphoapantetheine adenylyltransferase PPAT/CoaD with AMP-PNP from… · the same entry in another collection · chain F against F, 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 A3LHH1
- Elsewhere: RCSB PDB 3X1K · PDBe 3X1K · UniProt A3LHH1
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