Research workbench
Folate ecf transporter: amppnp bound state
Analyse Folate ecf transporter: amppnp bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D3M
- Type
- protein
- Length
- 1,976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Energy-coupling factor transporter ATP-binding protein ECFA1; Energy-coupling factor…
- EC
- 3.6.3.-
- UniProt
- Q1GBJ0, Q1GBI9, Q1G929, A0A061BSU4
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Energy-coupling factor transporter ATP-binding protein ECFA1 (EC 3.6.3.-) | protein | 280 | 39% helix, 15% strand | Q1GBJ0 |
| B, F | Energy-coupling factor transporter ATP-binding protein ECFA2 (EC 3.6.3.-) | protein | 281 | 38% helix, 19% strand | Q1GBI9 |
| C, G | S-component for folate | protein | 168 | 67% helix, 1% strand | Q1G929 |
| D, H | Energy-coupling factor transporter transmembrane protein ecft | protein | 259 | 63% helix, 0% strand | A0A061BSU4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, E, F
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 | 1041 | 0.83 | 0.85 | 116 | empty |
| 2 | 611 | 0.80 | 0.85 | 60 | empty |
| 3 | 166 | 0.79 | 0.94 | 24 | empty |
| 4 | 443 | 0.79 | 0.87 | 49 | empty |
| 5 | 664 | 0.78 | 0.83 | 58 | empty |
Interfaces
16 interfaces between chains.
- C–D · 2658 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 2653 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 1397 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1386 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1281 Ų buried · 5 hydrogen bonds · 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 F against A, TM-score 0.98
- Q1GBJ0 · AlphaFold monomer V2.0 prediction for energy-coupling factor transporter ATP-binding… · a predicted model of the same protein · chain E against A, TM-score 0.94
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 A0A061BSU4
- Elsewhere: RCSB PDB 5D3M · PDBe 5D3M · UniProt Q1GBJ0 · UniProt Q1GBI9 · UniProt Q1G929 · UniProt A0A061BSU4
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