Research workbench
Structure of ArhGAP12 bound to G-Actin
Analyse Structure of ArhGAP12 bound to G-Actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GVC
- Type
- protein
- Length
- 2,308 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Mus musculus; Oryctolagus cuniculus
- Molecule
- Actin, alpha skeletal muscle; Rho GTPase-activating protein 12
- UniProt
- P68135, Q8C0D4
- Ligands
- LAB, ATP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.6 · 7 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Actin, alpha skeletal muscle | protein | 359 | 45% helix, 21% strand | P68135 |
| A | Actin, alpha skeletal muscle | protein | 356 | 47% helix, 20% strand | P68135 |
| D | Actin, alpha skeletal muscle | protein | 356 | 45% helix, 21% strand | P68135 |
| R | Rho GTPase-activating protein 12 | protein | 216 | 65% helix, 0% strand | Q8C0D4 |
| Q | Rho GTPase-activating protein 12 | protein | 223 | 64% helix, 0% strand | Q8C0D4 |
| S | Rho GTPase-activating protein 12 | protein | 217 | 64% helix, 0% strand | Q8C0D4 |
| T | Rho GTPase-activating protein 12 | protein | 222 | 65% helix, 0% strand | Q8C0D4 |
Ligands and binding sites
- LAB · Latrunculin B · ligand · 4 copies · chains B, A, C, D
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains B, A, C, D
- MG · Magnesium ion · metal · 4 copies · chains B, A, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains B, R, A, S, C, T, D, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.78 | 0.80 | 94 | LAB, ATP, MG |
| 2 | 736 | 0.77 | 0.82 | 75 | EDO |
| 3 | 553 | 0.77 | 0.83 | 49 | EDO |
| 4 | 459 | 0.76 | 0.85 | 42 | EDO |
| 5 | 367 | 0.75 | 0.86 | 45 | LAB, ATP, MG |
Interfaces
11 interfaces between chains.
- D–Q · 1811 Ų buried · 16 hydrogen bonds · protein-protein
- C–T · 1796 Ų buried · 14 hydrogen bonds · protein-protein
- A–S · 1700 Ų buried · 14 hydrogen bonds · protein-protein
- B–R · 1630 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 569 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P68135
- Every structure of UniProt Q8C0D4
- Elsewhere: RCSB PDB 6GVC · PDBe 6GVC · UniProt P68135 · UniProt Q8C0D4
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