Research workbench
Crystal structure of a putative secreted protein (EUBREC_3654) from eubacterium rectale at 2.43 a resolution
Analyse Crystal structure of a putative secreted protein (EUBREC_3654) from eubacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LR4
- Type
- protein
- Length
- 1,381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- C4ZEB7
- Ligands
- PO4, CL
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Hypothetical protein | protein | 345 | 9% helix, 46% strand | C4ZEB7 |
| C | Hypothetical protein | protein | 346 | 9% helix, 46% strand | C4ZEB7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.72 | 0.79 | 53 | GOL |
| 2 | 52 | 0.64 | 0.94 | 20 | empty |
| 3 | 191 | 0.49 | 0.76 | 27 | empty |
| 4 | 165 | 0.43 | 0.74 | 27 | empty |
| 5 | 85 | 0.42 | 0.79 | 19 | CL |
Interfaces
3 interfaces between chains.
- C–D · 1042 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 598 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 260 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4LR4 · Crystal structure of a putative secreted protein (EUBREC_3654) from Eubacterium rectale… · 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 C4ZEB7
- Elsewhere: RCSB PDB 4LR4 · PDBe 4LR4 · UniProt C4ZEB7
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