Research workbench
Cryo-EM structure of the folate-specific ECF transporter complex in MSP2N2 lipid nanodiscs bound to ATP and ADP
Analyse Cryo-EM structure of the folate-specific ECF transporter complex in MSP2N2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BMP
- Type
- protein
- Length
- 989 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002
- Molecule
- Energy-coupling factor transporter ATP-binding protein EcfA1; Energy-coupling factor…
- EC
- 7.-.-.-, 3.6.3.-
- UniProt
- Q1GBJ0, Q1GBI9, Q1G929, Q1GBI8
- Ligands
- ATP, ADP, MG
- Pockets
- 14 · best druggability 0.79
Structure
electron microscopy · resolution 3.2 · 4 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Energy-coupling factor transporter ATP-binding protein EcfA1 (EC 7.-.-.-) | protein | 278 | 38% helix, 16% strand | Q1GBJ0 |
| B | Energy-coupling factor transporter ATP-binding protein EcfA2 (EC 3.6.3.-) | protein | 281 | 38% helix, 21% strand | Q1GBI9 |
| C | Folate family ECF transporter S component | protein | 169 | 75% helix, 4% strand | Q1G929 |
| D | Energy-coupling factor transporter transmembrane protein EcfT | protein | 261 | 70% helix, 3% strand | Q1GBI8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, C
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.79 | 0.80 | 57 | empty |
| 2 | 714 | 0.75 | 0.80 | 77 | empty |
| 3 | 503 | 0.75 | 0.83 | 70 | ATP, MG |
| 4 | 436 | 0.73 | 0.83 | 62 | empty |
| 5 | 70 | 0.55 | 0.87 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3086 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1437 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1142 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 770 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 241 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- Q1GBI9 · AlphaFold monomer V2.0 prediction for energy-coupling factor transporter ATP-binding… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q1GBJ0 · AlphaFold monomer V2.0 prediction for energy-coupling factor transporter ATP-binding… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q1GBJ0
- Every structure of UniProt Q1GBI9
- Every structure of UniProt Q1G929
- Every structure of UniProt Q1GBI8
- Elsewhere: RCSB PDB 8BMP · PDBe 8BMP · UniProt Q1GBJ0 · UniProt Q1GBI9 · UniProt Q1G929 · UniProt Q1GBI8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.