Research workbench
Crystal structure of the hypothetical lipoprotein ymcc from escherichia COLI (K12), northeast structural genomics target ER552.
Analyse Crystal structure of the hypothetical lipoprotein ymcc from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IN5
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical lipoprotein ymcc
- UniProt
- P75884
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical lipoprotein ymcc | protein | 195 | 14% helix, 53% strand | P75884 |
| B | Hypothetical lipoprotein ymcc | protein | 188 | 10% helix, 57% strand | P75884 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.45 | 0.81 | 20 | empty |
| 2 | 123 | 0.42 | 0.76 | 23 | empty |
| 3 | 94 | 0.41 | 0.77 | 16 | empty |
| 4 | 70 | 0.32 | 0.75 | 18 | empty |
| 5 | 57 | 0.29 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1324 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2IN5 · Crystal Structure of the hypothetical lipoprotein YmcC from Escherichia coli (K12)… · the same entry in another collection · chain A against A, TM-score 1.00
- P75884 · AlphaFold monomer V2.0 prediction for uncharacterized lipoprotein gfcb (P75884) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P75884
- Elsewhere: RCSB PDB 2IN5 · PDBe 2IN5 · UniProt P75884
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