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Crystal structure of E. COLI phosphatase yrbi, with mg, tetragonal form
Analyse Crystal structure of E. COLI phosphatase yrbi, with mg, tetragonal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HYC
- Type
- protein
- Length
- 1,436 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
- EC
- 3.1.3.45
- UniProt
- P67653
- Ligands
- MG, CL
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F, G, H | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45) | protein | 181 | 38% helix, 23% strand | P67653 |
| B | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45) | protein | 174 | 39% helix, 20% strand | P67653 |
| D | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45) | protein | 176 | 38% helix, 19% strand | P67653 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, H, F, G
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.73 | 0.76 | 123 | MG, CL |
| 2 | 1163 | 0.72 | 0.76 | 108 | empty |
| 3 | 328 | 0.62 | 0.79 | 33 | MG |
| 4 | 262 | 0.61 | 0.80 | 53 | empty |
| 5 | 311 | 0.61 | 0.79 | 58 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1181 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1178 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1169 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1169 Ų buried · 22 hydrogen bonds · protein-protein
- E–H · 1109 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3HYC · Crystal structure of E. coli phosphatase YrbI, with Mg, tetragonal form · the same entry in another collection · chain H against H, TM-score 1.00
- P67653 · AlphaFold monomer V2.0 prediction for 3-deoxy-D-manno-octulosonate 8-phosphate… · a predicted model of the same protein · chain D 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 P67653
- Elsewhere: RCSB PDB 3HYC · PDBe 3HYC · UniProt P67653
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