MolNFT v2 · #224999 · protein
Cryo-EM structure of the ATP-bound Mtb DppABCD with the D445A mutation of DppA
8XFC · Probable dipeptide-transport integral membrane protein ABC…: “Cryo-EM structure of the ATP-bound Mtb DppABCD with the D445A mutation of DppA”. Electron microscopy at 3.89, 1 ligand (ATP), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 8XFC
- Type
- protein
- Length
- 1,626 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.89
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- Probable dipeptide-transport integral membrane protein ABC transporter DppB; Probable…
- UniProt
- I6YGV9, L0TEV4, I6Y482, I6X811
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.89 · 4 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Probable dipeptide-transport integral membrane protein ABC transporter DppB | protein | 308 | 71% helix, 0% strand | I6YGV9 |
| C | Probable dipeptide-transport integral membrane protein ABC transporter DppC | protein | 284 | 67% helix, 0% strand | L0TEV4 |
| D | Probable dipeptide-transport ATP-binding protein ABC transporter DppD | protein | 517 | 31% helix, 17% strand | I6Y482 |
| A | Probable periplasmic dipeptide-binding lipoprotein DppA | protein | 517 | 27% helix, 18% strand | I6X811 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.84 | 0.85 | 78 | empty |
| 2 | 1153 | 0.80 | 0.81 | 109 | empty |
| 3 | 317 | 0.75 | 0.87 | 43 | empty |
| 4 | 620 | 0.75 | 0.82 | 72 | empty |
| 5 | 69 | 0.73 | 0.97 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2213 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1217 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 1038 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 996 Ų buried · 5 hydrogen bonds · protein-protein
- C–A · 238 Ų buried · 1 hydrogen bond · protein-protein
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 I6YGV9
- Every structure of UniProt L0TEV4
- Every structure of UniProt I6Y482
- Every structure of UniProt I6X811
- Elsewhere: RCSB PDB 8XFC · PDBe 8XFC · UniProt I6YGV9 · UniProt L0TEV4 · UniProt I6Y482 · UniProt I6X811
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