Research workbench
Crystal structure of native rhcc (YP_702633.1) from rhodococcus jostii RHA1 at 1.78 ångström
Analyse Crystal structure of native rhcc (YP_702633.1) from rhodococcus jostii RHA1 at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U5P
- Type
- protein
- Length
- 422 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhcc
- UniProt
- Q0SDB1
- Ligands
- MG
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhcc | protein | 140 | 35% helix, 28% strand | Q0SDB1 |
| B, C | Rhcc | protein | 141 | 35% helix, 28% strand | Q0SDB1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B, C
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, C, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.60 | 0.83 | 17 | empty |
| 2 | 139 | 0.58 | 0.83 | 17 | empty |
| 3 | 114 | 0.54 | 0.82 | 18 | empty |
| 4 | 202 | 0.51 | 0.76 | 22 | empty |
| 5 | 86 | 0.40 | 0.78 | 17 | B3P |
Interfaces
3 interfaces between chains.
- B–C · 1333 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1311 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1289 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4U5P · Crystal structure of native RhCC (YP_702633.1) from Rhodococcus jostii RHA1 at 1.78… · 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 Q0SDB1
- Elsewhere: RCSB PDB 4U5P · PDBe 4U5P · UniProt Q0SDB1
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