Research workbench
Structure of the E. COLI C-P lyase core complex
Analyse Structure of the E. COLI C-P lyase core complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XB6
- Type
- protein
- Length
- 1,940 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit phng; Alpha-D-ribose…
- EC
- 2.7.8.37, 4.7.1.1
- UniProt
- P16685, P16686, P16687, P16688
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit phng (EC 2.7.8.37) | protein | 144 | 49% helix, 31% strand | P16685 |
| B | Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit phnh (EC 2.7.8.37) | protein | 194 | 30% helix, 19% strand | P16686 |
| C, G | Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit phni (EC 2.7.8.37) | protein | 353 | 42% helix, 16% strand | P16687 |
| D, H | Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase (EC 4.7.1.1) | protein | 277 | 30% helix, 20% strand | P16688 |
| E | Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit phng (EC 2.7.8.37) | protein | 149 | 50% helix, 30% strand | P16685 |
| F | Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit phnh (EC 2.7.8.37) | protein | 193 | 31% helix, 20% strand | P16686 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, D, G, H
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.82 | 0.86 | 67 | ZN, SO4 |
| 2 | 715 | 0.82 | 0.85 | 71 | ZN, SO4 |
| 3 | 130 | 0.81 | 0.98 | 28 | empty |
| 4 | 124 | 0.78 | 0.96 | 29 | empty |
| 5 | 502 | 0.78 | 0.85 | 66 | empty |
Interfaces
15 interfaces between chains.
- C–G · 7108 Ų buried · 78 hydrogen bonds · protein-protein
- A–C · 3095 Ų buried · 51 hydrogen bonds · protein-protein
- E–G · 3092 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 2361 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2314 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- P16687 · AlphaFold monomer V2.0 prediction for alpha-D-ribose 1-methylphosphonate 5-triphosphate… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P16686 · AlphaFold monomer V2.0 prediction for alpha-D-ribose 1-methylphosphonate 5-triphosphate… · a predicted model of the same protein · chain F against A, TM-score 0.99
- P16688 · AlphaFold monomer V2.0 prediction for alpha-D-ribose 1-methylphosphonate 5-phosphate C-P… · a predicted model of the same protein · chain D against A, TM-score 0.98
- P16685 · AlphaFold monomer V2.0 prediction for alpha-D-ribose 1-methylphosphonate 5-triphosphate… · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P16685
- Every structure of UniProt P16686
- Every structure of UniProt P16687
- Every structure of UniProt P16688
- Elsewhere: RCSB PDB 4XB6 · PDBe 4XB6 · UniProt P16685 · UniProt P16686 · UniProt P16687 · UniProt P16688
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