MolNFT v1 · #163956 · protein
Crystal structure of IBPAFIC2 covalently tethered to CDC42
6SIU · Protein adenylyltransferase and cysteine protease ibpa: “Crystal structure of IBPAFIC2 covalently tethered to CDC42”. X-ray diffraction, 3 ligands (GDP, LJN, SO4), 14 pockets (best druggability 0.88). MolNFT v1 #163956 on GenesisL1…
- PDB
- 6SIU
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein adenylyltransferase and cysteine protease ibpa; Cell division control protein 42…
- EC
- 2.7.7.-, 3.4.22.-, 3.6.5.2
- UniProt
- Q06277, P60953
- Ligands
- GDP, LJN, SO4
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein adenylyltransferase and cysteine protease ibpa (EC 2.7.7.-, 3.4.22.-) | protein | 295 | 62% helix, 3% strand | Q06277 |
| B | Protein adenylyltransferase and cysteine protease ibpa (EC 2.7.7.-, 3.4.22.-) | protein | 297 | 63% helix, 3% strand | Q06277 |
| C | Cell division control protein 42 homolog (EC 3.6.5.2) | protein | 191 | 37% helix, 22% strand | P60953 |
| D | Cell division control protein 42 homolog (EC 3.6.5.2) | protein | 179 | 40% helix, 21% strand | P60953 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, C, A, D
- LJN · [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2, 3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · 2 copies · chains B, C, A, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, D, C
- GOL · Glycerol · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.88 | 0.90 | 117 | GOL, GDP |
| 2 | 524 | 0.66 | 0.77 | 61 | GDP, SO4 |
| 3 | 113 | 0.59 | 0.85 | 22 | empty |
| 4 | 299 | 0.59 | 0.78 | 31 | SO4 |
| 5 | 315 | 0.58 | 0.77 | 35 | SO4, LJN |
Interfaces
5 interfaces between chains.
- B–C · 1231 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1178 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1080 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 190 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6SIU · Crystal structure of IbpAFic2 covalently tethered to Cdc42 · the same entry in another collection · chain A against A, TM-score 1.00
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q06277
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 6SIU · PDBe 6SIU · UniProt Q06277 · UniProt P60953
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