Research workbench
The crystal structure of a conserved protein from planctomyces limnophilus dsm 3776
Analyse The crystal structure of a conserved protein from planctomyces limnophilus dsm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ROB
- Type
- protein
- Length
- 519 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized conserved protein
- UniProt
- D5SZ41
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized conserved protein | protein | 131 | 32% helix, 47% strand | D5SZ41 |
| B | Uncharacterized conserved protein | protein | 129 | 31% helix, 47% strand | D5SZ41 |
| D | Uncharacterized conserved protein | protein | 128 | 30% helix, 48% strand | D5SZ41 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.78 | 0.84 | 47 | GOL |
| 2 | 467 | 0.77 | 0.84 | 42 | GOL |
| 3 | 480 | 0.76 | 0.84 | 42 | GOL |
| 4 | 437 | 0.74 | 0.83 | 40 | GOL |
| 5 | 251 | 0.58 | 0.78 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1108 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1059 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 464 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3ROB · The crystal structure of a conserved protein from Planctomyces limnophilus DSM 3776 · 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 D5SZ41
- Elsewhere: RCSB PDB 3ROB · PDBe 3ROB · UniProt D5SZ41
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