Research workbench
Crystal structure of human ppcs in complex with P-hopan and amppnp
Analyse Crystal structure of human ppcs in complex with P-hopan and amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EDZ
- Type
- protein
- Length
- 1,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantothenate--cysteine ligase
- EC
- 6.3.2.51
- UniProt
- Q9HAB8
- Ligands
- ANP, J1O, MG, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Phosphopantothenate--cysteine ligase (EC 6.3.2.51) | protein | 305 | 42% helix, 22% strand | Q9HAB8 |
| C | Phosphopantothenate--cysteine ligase (EC 6.3.2.51) | protein | 304 | 41% helix, 22% strand | Q9HAB8 |
| B | Phosphopantothenate--cysteine ligase (EC 6.3.2.51) | protein | 306 | 44% helix, 25% strand | Q9HAB8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains D, C, B, A
- J1O · 4-[[(2R)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]butanoic acid · ligand · 4 copies · chains D, C, B, A
- MG · Magnesium ion · metal · 4 copies · chains D, C, B, A
- SO4 · Sulfate ion · ion · 9 copies · chains D, C, B, A
- GOL · Glycerol · additive · 5 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.82 | 0.84 | 75 | ANP, J1O, MG |
| 2 | 1114 | 0.79 | 0.81 | 94 | ANP, J1O, MG |
| 3 | 835 | 0.77 | 0.80 | 74 | SO4 |
| 4 | 459 | 0.76 | 0.84 | 42 | ANP, MG, J1O |
| 5 | 449 | 0.75 | 0.84 | 43 | ANP, J1O, MG |
Interfaces
6 interfaces between chains.
- B–A · 3288 Ų buried · 45 hydrogen bonds · protein-protein
- D–C · 339 Ų buried · 3 hydrogen bonds · protein-protein
- D–B · 165 Ų buried · 0 hydrogen bonds · protein-protein
- C–A · 151 Ų buried · 0 hydrogen bonds · protein-protein
- D–A · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7EDZ · Crystal Structure of human PPCS in complex with P-HoPan and AMPPNP · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HAB8 · AlphaFold monomer V2.0 prediction for phosphopantothenate--cysteine ligase (Q9HAB8) · a predicted model of the same protein · chain D 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 Q9HAB8
- Elsewhere: RCSB PDB 7EDZ · PDBe 7EDZ · UniProt Q9HAB8
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