MolNFT v1 · #136870 · protein
Crystal structure of the second beta-prism domain of rbmc from V. cholerae
5V6C · Hemolysin-related protein: “Crystal structure of the second beta-prism domain of rbmc from V. cholerae”. X-ray diffraction, 2 pockets (best druggability 0.58). MolNFT v1 #136870 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5V6C
- Type
- protein
- Length
- 402 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemolysin-related protein
- UniProt
- Q9KTH2
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemolysin-related protein | protein | 135 | 2% helix, 56% strand | Q9KTH2 |
| B | Hemolysin-related protein | protein | 138 | 2% helix, 55% strand | Q9KTH2 |
| C | Hemolysin-related protein | protein | 129 | 2% helix, 57% strand | Q9KTH2 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.58 | 0.76 | 52 | empty |
| 2 | 70 | 0.29 | 0.73 | 20 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 612 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V6C · Crystal Structure of the Second beta-Prism Domain of RbmC from V. cholerae · 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 Q9KTH2
- Elsewhere: RCSB PDB 5V6C · PDBe 5V6C · UniProt Q9KTH2
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