Research workbench
Crystal structure of YPT7 covalently modified with gnp
Analyse Crystal structure of YPT7 covalently modified with gnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHH
- Type
- protein
- Length
- 678 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein YPT7
- UniProt
- P32939
- Ligands
- 2UK, MG, CL
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding protein YPT7 | protein | 172 | 36% helix, 24% strand | P32939 |
| B | GTP-binding protein YPT7 | protein | 172 | 36% helix, 27% strand | P32939 |
| C | GTP-binding protein YPT7 | protein | 169 | 33% helix, 21% strand | P32939 |
| D | GTP-binding protein YPT7 | protein | 165 | 34% helix, 24% strand | P32939 |
Ligands and binding sites
- 2UK · 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-N-[3-(propanoylamino)propyl]guanosine · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.67 | 0.76 | 73 | 2UK, MG |
| 2 | 177 | 0.54 | 0.79 | 34 | 2UK, MG |
| 3 | 130 | 0.48 | 0.79 | 28 | 2UK, MG |
| 4 | 203 | 0.46 | 0.74 | 21 | empty |
| 5 | 51 | 0.38 | 0.81 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 544 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 112 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
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 P32939
- Elsewhere: RCSB PDB 4PHH · PDBe 4PHH · UniProt P32939
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