Research workbench
Cryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the inward facing apo state
Analyse Cryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8IPQ
- Type
- protein
- Length
- 1,996 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Mycolicibacterium smegmatis
- Molecule
- Transmembrane ATP-binding protein ABC transporter cydD; Component linked with the…
- EC
- 3.6.3.25
- UniProt
- A0A8B4R4Z5, A0A8B4R833
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.5 · 2 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Transmembrane ATP-binding protein ABC transporter cydD (EC 3.6.3.25) | protein | 505 | 63% helix, 7% strand | A0A8B4R4Z5 |
| A, D | Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC | protein | 493 | 62% helix, 4% strand | A0A8B4R833 |
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 | 1121 | 0.86 | 0.87 | 107 | empty |
| 2 | 1113 | 0.85 | 0.86 | 112 | empty |
| 3 | 126 | 0.79 | 0.97 | 31 | empty |
| 4 | 126 | 0.79 | 0.96 | 33 | empty |
| 5 | 540 | 0.71 | 0.80 | 49 | empty |
Interfaces
4 interfaces between chains.
- B–A · 4902 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 4877 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 859 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 3 hydrogen bonds · 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 A0A8B4R4Z5
- Every structure of UniProt A0A8B4R833
- Elsewhere: RCSB PDB 8IPQ · PDBe 8IPQ · UniProt A0A8B4R4Z5 · UniProt A0A8B4R833
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