MolNFT v1 · #78546 · protein
2.65 ångström resolution crystal structure of dtdp-4-dehydrorhamnose reductase (rfbd) from bacillus anthracis str. ames in complex with NADP
3SC6: “2.65 ångström resolution crystal structure of dtdp-4-dehydrorhamnose reductase (rfbd) from bacillus anthracis…”. X-ray diffraction, 2 ligands (NAP, SO4), 13 pockets (best druggability 0.80). MolNFT v1 #78546 on GenesisL1: 3D…
- PDB
- 3SC6
- Type
- protein
- Length
- 1,684 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose reductase
- EC
- 1.1.1.133
- UniProt
- Q81TN9
- Ligands
- NAP, SO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 281 | 42% helix, 20% strand | Q81TN9 |
| B | Dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 280 | 41% helix, 19% strand | Q81TN9 |
| C, F | Dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 281 | 41% helix, 20% strand | Q81TN9 |
| D | Dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 283 | 40% helix, 20% strand | Q81TN9 |
| E | Dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 278 | 41% helix, 21% strand | Q81TN9 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.80 | 0.81 | 100 | empty |
| 2 | 1070 | 0.79 | 0.81 | 93 | empty |
| 3 | 703 | 0.74 | 0.80 | 62 | NAP, SO4 |
| 4 | 732 | 0.74 | 0.79 | 57 | NAP, SO4 |
| 5 | 679 | 0.73 | 0.79 | 57 | NAP, SO4 |
Interfaces
9 interfaces between chains.
- D–E · 680 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 650 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 645 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 626 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3SC6 · 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD)… · 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 Q81TN9
- Elsewhere: RCSB PDB 3SC6 · PDBe 3SC6 · UniProt Q81TN9
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