MolNFT v1 · #171767 · protein
The structure of ecf pant transporter in a complex with a nanobody
6ZG3 · Energy-coupling factor transporter ATP-binding protein ECFA1: “The structure of ecf pant transporter in a complex with a nanobody”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #171767 on GenesisL1: 3D…
- PDB
- 6ZG3
- Type
- protein
- Length
- 2,309 residues
- Chains
- 10
- 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
- 7.-.-.-, 3.6.3.-
- UniProt
- Q1GBJ0, Q1GBI9, Q1GBG0, Q1GBI8
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Energy-coupling factor transporter ATP-binding protein ECFA1 (EC 7.-.-.-) | protein | 280 | 42% helix, 21% strand | Q1GBJ0 |
| B | Energy-coupling factor transporter ATP-binding protein ECFA2 (EC 3.6.3.-) | protein | 282 | 42% helix, 19% strand | Q1GBI9 |
| C, H | Conserved hypothetical membrane protein | protein | 207 | 76% helix, 1% strand | Q1GBG0 |
| D, I | Putative cobalt ABC transporter, permease protein | protein | 260 | 70% helix, 0% strand | Q1GBI8 |
| E | CA14381 nanobody | protein | 126 | 5% helix, 45% strand | — |
| F | Energy-coupling factor transporter ATP-binding protein ECFA1 (EC 7.-.-.-) | protein | 279 | 43% helix, 20% strand | Q1GBJ0 |
| G | Energy-coupling factor transporter ATP-binding protein ECFA2 (EC 3.6.3.-) | protein | 283 | 42% helix, 20% strand | Q1GBI9 |
| J | CA14381 nanobody | protein | 125 | 5% helix, 47% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, F, C, D, E, I, J
- LMT · Dodecyl-beta-D-maltoside · additive · 7 copies · chains C, D, G, H, I
- CIT · Citric acid · additive · 2 copies · chains C, H
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 | 1112 | 0.85 | 0.86 | 121 | PEG |
| 2 | 1152 | 0.82 | 0.83 | 105 | LMT, CIT |
| 3 | 236 | 0.81 | 0.94 | 35 | CIT |
| 4 | 526 | 0.80 | 0.86 | 65 | empty |
| 5 | 987 | 0.79 | 0.80 | 68 | LMT |
Interfaces
23 interfaces between chains.
- H–I · 2219 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 2212 Ų buried · 5 hydrogen bonds · protein-protein
- A–I · 1511 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1504 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1325 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6ZG3 · the structure of ECF PanT transporter in a complex with a nanobody · the same entry in another collection · chain J against J, TM-score 1.00
- 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 0.97
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 Q1GBG0
- Every structure of UniProt Q1GBI8
- Elsewhere: RCSB PDB 6ZG3 · PDBe 6ZG3 · UniProt Q1GBJ0 · UniProt Q1GBI9 · UniProt Q1GBG0 · UniProt Q1GBI8
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