Research workbench
Crystal structure of GIT1 pbd domain in complex with liprin-ALPHA2
Analyse Crystal structure of GIT1 pbd domain in complex with liprin-ALPHA2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IUH
- Type
- protein
- Length
- 310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arf GTPase-activating protein GIT1; Liprin-alpha-2
- UniProt
- Q9Z272, O75334
- Ligands
- IOD
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arf GTPase-activating protein GIT1 | protein | 123 | 76% helix, 0% strand | Q9Z272 |
| B | Arf GTPase-activating protein GIT1 | protein | 118 | 81% helix, 0% strand | Q9Z272 |
| C | Liprin-alpha-2 | protein | 34 | 65% helix, 0% strand | O75334 |
| D | Liprin-alpha-2 | protein | 35 | 63% helix, 0% strand | O75334 |
Ligands and binding sites
- IOD · Iodide ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.46 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1137 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1063 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 383 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6IUH · Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Z272 · AlphaFold monomer V2.0 prediction for arf GTPase-activating protein GIT1 (Q9Z272) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O75334 · AlphaFold monomer V2.0 prediction for liprin-alpha-2 (O75334) · a predicted model of the same protein · chain C against A, TM-score 0.73
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 Q9Z272
- Every structure of UniProt O75334
- Elsewhere: RCSB PDB 6IUH · PDBe 6IUH · UniProt Q9Z272 · UniProt O75334
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