Research workbench
Structure of the dtdp-4-keto-L-rhamnose reductase related protein (other form) from thermus thermophilus HB8
Analyse Structure of the dtdp-4-keto-L-rhamnose reductase related protein (other form)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CQ3
- Type
- protein
- Length
- 490 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein TTHB138
- UniProt
- Q53W28
- Ligands
- MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Putative uncharacterized protein TTHB138 | protein | 98 | 31% helix, 23% strand | Q53W28 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, E, C, D
- GOL · Glycerol · additive · 11 copies · chains A, B, E, C, D
- P6G · Hexaethylene glycol · additive · chains A, C
- PG4 · Tetraethylene glycol · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.76 | 0.79 | 92 | GOL |
| 2 | 536 | 0.72 | 0.81 | 55 | empty |
| 3 | 178 | 0.50 | 0.77 | 19 | GOL |
| 4 | 168 | 0.49 | 0.77 | 19 | GOL |
| 5 | 99 | 0.48 | 0.81 | 16 | empty |
Interfaces
7 interfaces between chains.
- B–C · 530 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 511 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 477 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 439 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3CQ3 · Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein (other form) 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
- Every structure of UniProt Q53W28
- Elsewhere: RCSB PDB 3CQ3 · PDBe 3CQ3 · UniProt Q53W28
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