Research workbench
Structure of the PHACTR1 rpel domain bound to G-actin
Analyse Structure of the PHACTR1 rpel domain 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
- 4B1Z
- Type
- protein
- Length
- 2,351 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Phosphatase and actin regulator 1
- UniProt
- P68135, G5E8P7
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 335 | 47% helix, 19% strand | P68135 |
| B, F | Actin, alpha skeletal muscle | protein | 357 | 45% helix, 20% strand | P68135 |
| C | Actin, alpha skeletal muscle | protein | 370 | 44% helix, 20% strand | P68135 |
| D | Actin, alpha skeletal muscle | protein | 356 | 46% helix, 20% strand | P68135 |
| E | Actin, alpha skeletal muscle | protein | 359 | 45% helix, 21% strand | P68135 |
| M | Phosphatase and actin regulator 1 | protein | 110 | 61% helix, 0% strand | G5E8P7 |
| N | Phosphatase and actin regulator 1 | protein | 107 | 60% helix, 0% strand | G5E8P7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, M, C, D, E, N, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 8 copies · chains A, B, C, E, N, F, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.85 | 0.87 | 116 | ATP, MG |
| 2 | 1045 | 0.84 | 0.85 | 108 | ATP, MG |
| 3 | 1069 | 0.83 | 0.84 | 106 | ATP, MG |
| 4 | 1155 | 0.81 | 0.82 | 109 | ATP, MG |
| 5 | 1044 | 0.81 | 0.82 | 95 | GOL |
Interfaces
16 interfaces between chains.
- F–N · 1670 Ų buried · 23 hydrogen bonds · protein-protein
- C–M · 1604 Ų buried · 18 hydrogen bonds · protein-protein
- B–M · 1470 Ų buried · 16 hydrogen bonds · protein-protein
- E–N · 1357 Ų buried · 17 hydrogen bonds · protein-protein
- A–M · 797 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 G5E8P7
- Elsewhere: RCSB PDB 4B1Z · PDBe 4B1Z · UniProt P68135 · UniProt G5E8P7
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