Research workbench
Crystal structure of putative isomerase from sinorhizobium meliloti, open loop conformation (target efi-502104)
Analyse Crystal structure of putative isomerase from sinorhizobium meliloti, open loop… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H1Z
- Type
- protein
- Length
- 3,034 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase Q92ZS5
- EC
- 6.-.-.-
- UniProt
- Q92ZS5
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enolase Q92ZS5 (EC 6.-.-.-) | protein | 376 | 43% helix, 22% strand | Q92ZS5 |
| B | Enolase Q92ZS5 (EC 6.-.-.-) | protein | 388 | 42% helix, 22% strand | Q92ZS5 |
| C, H | Enolase Q92ZS5 (EC 6.-.-.-) | protein | 378 | 42% helix, 22% strand | Q92ZS5 |
| D | Enolase Q92ZS5 (EC 6.-.-.-) | protein | 379 | 44% helix, 22% strand | Q92ZS5 |
| E | Enolase Q92ZS5 (EC 6.-.-.-) | protein | 381 | 42% helix, 23% strand | Q92ZS5 |
| F | Enolase Q92ZS5 (EC 6.-.-.-) | protein | 374 | 44% helix, 22% strand | Q92ZS5 |
| G | Enolase Q92ZS5 (EC 6.-.-.-) | protein | 380 | 43% helix, 22% strand | Q92ZS5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 5 copies · chains B, F, A, C, D, H, E, G
- FMT · Formic acid · additive · 7 copies · chains A, B, C, E, F, G, H
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.86 | 0.91 | 70 | CL |
| 2 | 674 | 0.86 | 0.90 | 87 | empty |
| 3 | 393 | 0.86 | 0.94 | 42 | empty |
| 4 | 615 | 0.86 | 0.91 | 81 | CL |
| 5 | 403 | 0.86 | 0.94 | 42 | empty |
Interfaces
16 interfaces between chains.
- D–H · 2319 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2292 Ų buried · 33 hydrogen bonds · protein-protein
- E–G · 2258 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 2252 Ų buried · 33 hydrogen bonds · protein-protein
- F–G · 1063 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4H1Z · Crystal structure of putative isomerase from Sinorhizobium meliloti, open loop… · 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 Q92ZS5
- Elsewhere: RCSB PDB 4H1Z · PDBe 4H1Z · UniProt Q92ZS5
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