MolNFT v1 · #114976 · protein
Crystal structure of human myosin 9B rhogap domain at 2.2 ångström
5C5S · Unconventional myosin-ixb: “Crystal structure of human myosin 9B rhogap domain at 2.2 ångström”. X-ray diffraction, 4 pockets (best druggability 0.77). MolNFT v1 #114976 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C5S
- Type
- protein
- Length
- 817 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-ixb
- UniProt
- Q13459
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unconventional myosin-ixb | protein | 210 | 62% helix, 0% strand | Q13459 |
| B | Unconventional myosin-ixb | protein | 202 | 64% helix, 0% strand | Q13459 |
| C | Unconventional myosin-ixb | protein | 202 | 63% helix, 0% strand | Q13459 |
| D | Unconventional myosin-ixb | protein | 203 | 63% helix, 0% strand | Q13459 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.77 | 0.79 | 111 | empty |
| 2 | 444 | 0.71 | 0.81 | 41 | empty |
| 3 | 493 | 0.68 | 0.79 | 63 | empty |
| 4 | 270 | 0.48 | 0.73 | 30 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1405 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1377 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 479 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 311 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C5S · Crystal Structure of human Myosin 9b RhoGAP domain at 2.2 angstrom · the same entry in another collection · chain D against D, TM-score 1.00
- Q13459 · AlphaFold monomer V2.0 prediction for unconventional myosin-ixb (Q13459) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q13459
- Elsewhere: RCSB PDB 5C5S · PDBe 5C5S · UniProt Q13459
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