Research workbench
Crystal structure of escherichia COLI gene product yecd at 1.3 a resolution
Analyse Crystal structure of escherichia COLI gene product yecd at 1.3 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J2R
- Type
- protein
- Length
- 748 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical isochorismatase family protein yecd
- UniProt
- P37347
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Hypothetical isochorismatase family protein yecd | protein | 188 | 35% helix, 21% strand | P37347 |
| B | Hypothetical isochorismatase family protein yecd | protein | 185 | 35% helix, 21% strand | P37347 |
| C | Hypothetical isochorismatase family protein yecd | protein | 187 | 35% helix, 21% strand | P37347 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.87 | 0.91 | 44 | empty |
| 2 | 383 | 0.71 | 0.82 | 36 | MPD |
| 3 | 355 | 0.71 | 0.83 | 40 | MPD |
| 4 | 378 | 0.70 | 0.82 | 36 | MPD |
| 5 | 380 | 0.70 | 0.82 | 41 | MPD |
Interfaces
6 interfaces between chains.
- C–D · 1894 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1832 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 760 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 746 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 162 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1J2R · Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution · 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 P37347
- Elsewhere: RCSB PDB 1J2R · PDBe 1J2R · UniProt P37347
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