Research workbench
The high resolution structures of rmlc from streptococcus suis in complex with dtdp-D-xylose
Analyse The high resolution structures of rmlc from streptococcus suis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NZC
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
- EC
- 5.1.3.13
- UniProt
- Q8GIQ0
- Ligands
- TDX, NI
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dtdp-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (EC 5.1.3.13) | protein | 196 | 14% helix, 40% strand | Q8GIQ0 |
| C, D | Dtdp-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (EC 5.1.3.13) | protein | 194 | 14% helix, 40% strand | Q8GIQ0 |
Ligands and binding sites
- TDX · Thymidine-5'-diphospho-beta-D-xylose · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.68 | 0.83 | 37 | TDX |
| 2 | 293 | 0.67 | 0.83 | 34 | TDX |
| 3 | 276 | 0.67 | 0.83 | 37 | TDX |
| 4 | 317 | 0.65 | 0.81 | 40 | TDX |
| 5 | 69 | 0.48 | 0.84 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1793 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1789 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1NZC · The high resolution structures of RmlC from Streptococcus suis in complex with… · 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 Q8GIQ0
- Elsewhere: RCSB PDB 1NZC · PDBe 1NZC · UniProt Q8GIQ0
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