Research workbench
Crystal structure of hldc from burkholderia pseudomallei
Analyse Crystal structure of hldc from burkholderia pseudomallei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X9Q
- Type
- protein
- Length
- 632 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cytidylyltransferase
- UniProt
- Q63XZ4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative cytidylyltransferase | protein | 158 | 45% helix, 19% strand | Q63XZ4 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.71 | 0.84 | 38 | MES |
| 2 | 444 | 0.71 | 0.81 | 40 | MES |
| 3 | 346 | 0.61 | 0.77 | 31 | empty |
| 4 | 376 | 0.60 | 0.76 | 36 | empty |
| 5 | 406 | 0.59 | 0.75 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1407 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1281 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 363 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 346 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 309 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X9Q · Crystal structure of HldC from Burkholderia pseudomallei · 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 Q63XZ4
- Elsewhere: RCSB PDB 5X9Q · PDBe 5X9Q · UniProt Q63XZ4
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