Research workbench
Crystal structure of a putative lipoprotein (RUMGNA_00858) from ruminococcus gnavus atcc 29149 at 1.76 a resolution
Analyse Crystal structure of a putative lipoprotein (RUMGNA_00858) from ruminococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IB2
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lipoprotein
- UniProt
- A7AZY4
- Ligands
- MET, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative lipoprotein | protein | 247 | 41% helix, 25% strand | A7AZY4 |
| B | Putative lipoprotein | protein | 243 | 40% helix, 24% strand | A7AZY4 |
Ligands and binding sites
- MET · Methionine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.76 | 0.81 | 59 | CL |
| 2 | 160 | 0.48 | 0.77 | 21 | empty |
| 3 | 53 | 0.40 | 0.81 | 17 | CL |
| 4 | 77 | 0.38 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 489 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4IB2 · Crystal structure of a putative lipoprotein (RUMGNA_00858) from Ruminococcus gnavus ATCC… · the same entry in another collection · chain B against B, 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 A7AZY4
- Elsewhere: RCSB PDB 4IB2 · PDBe 4IB2 · UniProt A7AZY4
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