MolNFT v1 · #139416 · protein
Crystal structure of semet-hldc from burkholderia pseudomallei
5XF2 · Putative cytidylyltransferase: “Crystal structure of semet-hldc from burkholderia pseudomallei”. X-ray diffraction, 18 pockets (best druggability 0.74). MolNFT v1 #139416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XF2
- Type
- protein
- Length
- 1,233 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cytidylyltransferase
- UniProt
- Q63XZ4
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative cytidylyltransferase | protein | 142 | 42% helix, 21% strand | Q63XZ4 |
| B, C, D, F, G, H | Putative cytidylyltransferase | protein | 158 | 44% helix, 19% strand | Q63XZ4 |
| E | Putative cytidylyltransferase | protein | 143 | 41% helix, 21% strand | Q63XZ4 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.74 | 0.85 | 37 | EPE |
| 2 | 315 | 0.72 | 0.85 | 39 | EPE |
| 3 | 472 | 0.69 | 0.80 | 37 | EPE |
| 4 | 388 | 0.68 | 0.80 | 36 | EPE |
| 5 | 428 | 0.62 | 0.76 | 35 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1287 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1283 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1107 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1090 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 373 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 5XF2 · Crystal structure of SeMet-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 5XF2 · PDBe 5XF2 · UniProt Q63XZ4
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