Research workbench
Cryo EM structure of the nucleotide free acinetobacter mlafedb complex
Analyse Cryo EM structure of the nucleotide free acinetobacter mlafedb complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D06
- 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
- PGV
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Intermembrane phospholipid transport system permease protein mlae | protein | 256 | 84% helix, 0% strand | V5V9F4 |
| B, E | ABC transporter ATP-binding protein | protein | 263 | 30% helix, 18% strand | A0A086HZU3 |
| C, F | Anti-sigma factor antagonist | protein | 95 | 31% helix, 16% strand | V5V9K5 |
| G, H, I, J, K, L | Mce family protein | protein | 191 | 29% helix, 24% strand | V5V921 |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 12 copies · chains A, D, H, I, G, L, K, J
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 | 425 | 0.81 | 0.89 | 44 | PGV |
| 2 | 819 | 0.79 | 0.82 | 80 | empty |
| 3 | 570 | 0.78 | 0.84 | 70 | empty |
| 4 | 816 | 0.76 | 0.79 | 64 | PGV |
| 5 | 725 | 0.75 | 0.81 | 94 | empty |
Interfaces
27 interfaces between chains.
- B–E · 2021 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1497 Ų buried · 0 hydrogen bonds · protein-protein
- I–J · 1212 Ų buried · 6 hydrogen bonds · protein-protein
- G–L · 1163 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 1060 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7D06 · Cryo EM structure of the nucleotide free Acinetobacter MlaFEDB complex · 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 7D06 · PDBe 7D06 · UniProt V5V9F4 · UniProt A0A086HZU3 · UniProt V5V9K5 · UniProt V5V921
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