Research workbench
Crystal structure of dtdp-4-dehydrorhamnose reductase from klebsiella pneumoniae with bound NADP
Analyse Crystal structure of dtdp-4-dehydrorhamnose reductase from klebsiella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CTR
- Type
- protein
- Length
- 1,191 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose reductase
- EC
- 1.1.1.133
- UniProt
- C9K1F1
- Ligands
- NAP, NA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 298 | 44% helix, 18% strand | C9K1F1 |
| D | Dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 297 | 45% helix, 18% strand | C9K1F1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.73 | 0.97 | 20 | empty |
| 2 | 579 | 0.71 | 0.79 | 56 | NAP |
| 3 | 551 | 0.70 | 0.79 | 54 | NAP |
| 4 | 512 | 0.70 | 0.79 | 57 | NAP |
| 5 | 590 | 0.69 | 0.78 | 53 | NAP |
Interfaces
3 interfaces between chains.
- A–B · 1147 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 553 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 8CTR · Crystal Structure of dTDP-4-dehydrorhamnose reductase from Klebsiella pneumoniae 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 C9K1F1
- Elsewhere: RCSB PDB 8CTR · PDBe 8CTR · UniProt C9K1F1
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