Research workbench
Crystal structure of IBPAFIC2-H3717A in complex with adenylylated CDC42
Analyse Crystal structure of IBPAFIC2-H3717A in complex with adenylylated CDC42 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITR
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine monophosphate-protein transferase and cysteine protease ibpa; Cell division…
- EC
- 2.7.7.1
- UniProt
- Q06277, P60953
- Ligands
- AMP, GDP, MG, SO4
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein transferase and cysteine protease ibpa (EC 2.7.7.1) | protein | 299 | 61% helix, 2% strand | Q06277 |
| B | Adenosine monophosphate-protein transferase and cysteine protease ibpa (EC 2.7.7.1) | protein | 296 | 62% helix, 2% strand | Q06277 |
| C | Cell division control protein 42 homolog | protein | 176 | 41% helix, 23% strand | P60953 |
| D | Cell division control protein 42 homolog | protein | 177 | 40% helix, 23% strand | P60953 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains B, C, A, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, C, A, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.89 | 0.91 | 145 | GDP, MG |
| 2 | 281 | 0.66 | 0.82 | 30 | AMP |
| 3 | 371 | 0.66 | 0.80 | 36 | AMP |
| 4 | 180 | 0.57 | 0.80 | 21 | SO4 |
| 5 | 102 | 0.56 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1289 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1210 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1045 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ITR · Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42 · the same entry in another collection · chain D against D, 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 0.96
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 4ITR · PDBe 4ITR · UniProt Q06277 · UniProt P60953
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