MolNFT v1 · #97414 · protein
Substrate binding domain of putative molybdenum ABC transporter from clostridium difficile
4KD5 · ABC-type transport system, molybdenum-specific…: “Substrate binding domain of putative molybdenum ABC transporter from clostridium difficile”. X-ray diffraction, 2 ligands (SBT, SO4), 12 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 4KD5
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type transport system, molybdenum-specific extracellular solute-binding protein
- UniProt
- Q18A64
- Ligands
- SBT, SO4
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | ABC-type transport system, molybdenum-specific extracellular solute-binding protein | protein | 229 | 38% helix, 26% strand | Q18A64 |
| B | ABC-type transport system, molybdenum-specific extracellular solute-binding protein | protein | 228 | 39% helix, 25% strand | Q18A64 |
| D | ABC-type transport system, molybdenum-specific extracellular solute-binding protein | protein | 227 | 39% helix, 25% strand | Q18A64 |
Ligands and binding sites
- SBT · 2-butanol · ligand · 3 copies · chains C, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- FMT · Formic acid · additive · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.69 | 0.80 | 57 | SBT |
| 2 | 445 | 0.69 | 0.81 | 55 | SO4 |
| 3 | 157 | 0.54 | 0.80 | 20 | FMT |
| 4 | 261 | 0.52 | 0.75 | 40 | empty |
| 5 | 143 | 0.45 | 0.77 | 33 | FMT |
Interfaces
4 interfaces between chains.
- A–D · 773 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 705 Ų buried · 5 hydrogen bonds · protein-protein
- C–A · 682 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 209 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4KD5 · substrate binding domain of putative molybdenum ABC transporter from Clostridium difficile · the same entry in another collection · chain C against C, 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 Q18A64
- Elsewhere: RCSB PDB 4KD5 · PDBe 4KD5 · UniProt Q18A64
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