MolNFT v1 · #153703 · protein
Crystal structure of GIT/PIX complex
6JMT · Arf GTPase-activating protein GIT2: “Crystal structure of GIT/PIX complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #153703 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JMT
- Type
- protein
- Length
- 2,170 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arf GTPase-activating protein GIT2; Beta pix
- UniProt
- Q80XR8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 55% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arf GTPase-activating protein GIT2 | protein | 347 | 55% helix, 3% strand | Q80XR8 |
| D | Arf GTPase-activating protein GIT2 | protein | 350 | 54% helix, 3% strand | Q80XR8 |
| B | Arf GTPase-activating protein GIT2 | protein | 349 | 55% helix, 3% strand | Q80XR8 |
| C | Arf GTPase-activating protein GIT2 | protein | 339 | 54% helix, 3% strand | Q80XR8 |
| E | Arf GTPase-activating protein GIT2 | protein | 343 | 55% helix, 3% strand | Q80XR8 |
| F | Arf GTPase-activating protein GIT2 | protein | 346 | 54% helix, 3% strand | Q80XR8 |
| I, J, K, L, M, N | Beta pix | protein | 16 | 81% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.83 | 0.84 | 101 | empty |
| 2 | 1059 | 0.83 | 0.83 | 101 | empty |
| 3 | 997 | 0.81 | 0.82 | 91 | empty |
| 4 | 1190 | 0.80 | 0.81 | 113 | empty |
| 5 | 945 | 0.78 | 0.81 | 99 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1124 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 1040 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 892 Ų buried · 8 hydrogen bonds · protein-protein
- D–N · 859 Ų buried · 2 hydrogen bonds · protein-protein
- B–M · 838 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6JMT · Crystal structure of GIT/PIX complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q80XR8
- Elsewhere: RCSB PDB 6JMT · PDBe 6JMT · UniProt Q80XR8
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