Research workbench
Crystal structure of possible sugar phosphatase, had superfamily (ZP_00311070.1) from cytophaga hutchinsonii atcc 33406 at 2.10 a resolution
Analyse Crystal structure of possible sugar phosphatase, had superfamily… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HX1
- Type
- protein
- Length
- 1,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted sugar phosphatases of the had superfamily
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Predicted sugar phosphatases of the had superfamily | protein | 284 | 40% helix, 23% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 15 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.72 | 0.83 | 51 | MG, CL, EPE |
| 2 | 385 | 0.71 | 0.83 | 43 | CL, EPE, EDO |
| 3 | 633 | 0.71 | 0.79 | 64 | CL, EPE, EDO |
| 4 | 346 | 0.71 | 0.83 | 44 | CL, EPE, EDO |
| 5 | 416 | 0.67 | 0.80 | 54 | CL, EDO |
Interfaces
4 interfaces between chains.
- A–C · 1378 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1348 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1028 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1008 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 2HX1 · Crystal structure of possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from… · 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
- Elsewhere: RCSB PDB 2HX1 · PDBe 2HX1
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