MolNFT v1 · #93776 · protein
Crystal structure of burkholderia pseudomallei effector protein chbp in complex with NEDD8
4HCP · Putative ATP/GTP binding protein: “Crystal structure of burkholderia pseudomallei effector protein chbp in complex with NEDD8”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.64). MolNFT v1 #93776 on GenesisL1: 3D…
- PDB
- 4HCP
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ATP/GTP binding protein; NEDD8
- UniProt
- Q63KH5, Q15843
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ATP/GTP binding protein | protein | 245 | 48% helix, 12% strand | Q63KH5 |
| B | NEDD8 | protein | 75 | 24% helix, 36% strand | Q15843 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.64 | 0.89 | 25 | empty |
| 2 | 149 | 0.43 | 0.76 | 31 | empty |
| 3 | 85 | 0.38 | 0.77 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 1240 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4HCP · crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q15843 · AlphaFold monomer V2.0 prediction for NEDD8 (Q15843) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q63KH5
- Every structure of UniProt Q15843
- Elsewhere: RCSB PDB 4HCP · PDBe 4HCP · UniProt Q63KH5 · UniProt Q15843
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