Research workbench
Acinetobacter mlafedb complex in ATP-bound VTRANS1 conformation
Analyse Acinetobacter mlafedb complex in ATP-bound VTRANS1 conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D08
- Type
- protein
- Length
- 2,374 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intermembrane phospholipid transport system permease protein mlae; ABC transporter…
- UniProt
- V5V9F4, A0A086HZU3, V5V9K5, V5V921
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Intermembrane phospholipid transport system permease protein mlae | protein | 256 | 77% helix, 0% strand | V5V9F4 |
| B, E | ABC transporter ATP-binding protein | protein | 263 | 32% helix, 16% strand | A0A086HZU3 |
| C, F | Anti-sigma factor antagonist | protein | 95 | 34% helix, 14% strand | V5V9K5 |
| G, H, I, J, K, L | Mce family protein | protein | 191 | 29% helix, 20% strand | V5V921 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.84 | 0.89 | 52 | empty |
| 2 | 602 | 0.82 | 0.87 | 85 | empty |
| 3 | 411 | 0.78 | 0.87 | 64 | empty |
| 4 | 552 | 0.76 | 0.83 | 70 | empty |
| 5 | 772 | 0.74 | 0.79 | 75 | empty |
Interfaces
31 interfaces between chains.
- B–E · 2050 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1642 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 1159 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1135 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 1068 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7D08 · Acinetobacter MlaFEDB complex in ATP-bound Vtrans1 conformation · 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 V5V9F4
- Every structure of UniProt A0A086HZU3
- Every structure of UniProt V5V9K5
- Every structure of UniProt V5V921
- Elsewhere: RCSB PDB 7D08 · PDBe 7D08 · UniProt V5V9F4 · UniProt A0A086HZU3 · UniProt V5V9K5 · UniProt V5V921
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