Research workbench
Crystal structure of the L780 udp-rhamnose synthase from acanthamoeba polyphaga mimivirus
Analyse Crystal structure of the L780 udp-rhamnose synthase from acanthamoeba polyphaga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JID
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-L-rhamnose synthase
- UniProt
- Q5UPS5
- Ligands
- AWU, NAP
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-L-rhamnose synthase | protein | 287 | 42% helix, 15% strand | Q5UPS5 |
| B | Udp-L-rhamnose synthase | protein | 287 | 41% helix, 15% strand | Q5UPS5 |
Ligands and binding sites
- AWU · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene) pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.82 | 0.87 | 63 | AWU, NAP |
| 2 | 639 | 0.82 | 0.87 | 68 | AWU, NAP |
| 3 | 191 | 0.53 | 0.78 | 34 | empty |
| 4 | 108 | 0.40 | 0.76 | 23 | empty |
| 5 | 85 | 0.35 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1041 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7JID · Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus · 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 Q5UPS5
- Elsewhere: RCSB PDB 7JID · PDBe 7JID · UniProt Q5UPS5
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