MolNFT v1 · #77471 · protein
Structure of a two-domain nrps fusion protein containing the ente adenylation domain and entb aryl-carrier protein from enterobactin biosynthesis
3RG2 · Enterobactin synthase component E (ente), 2,3-dihydro-2,3…: “Structure of a two-domain nrps fusion protein containing the ente adenylation domain and entb aryl-carrier…”. X-ray diffraction, 3 ligands (SVS, PNS, IOD), 20 pockets…
- PDB
- 3RG2
- Type
- protein
- Length
- 6,078 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase…
- EC
- 2.7.7.58, 2.3.1.-
- UniProt
- P10378, Q1REW7
- Ligands
- SVS, PNS, IOD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 611 | 36% helix, 22% strand | P10378, Q1REW7 |
| B | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 606 | 36% helix, 23% strand | P10378, Q1REW7 |
| C | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 613 | 36% helix, 23% strand | P10378, Q1REW7 |
| D | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 607 | 36% helix, 23% strand | P10378, Q1REW7 |
| E | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 610 | 36% helix, 23% strand | P10378, Q1REW7 |
| F | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 604 | 36% helix, 23% strand | P10378, Q1REW7 |
| G | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 602 | 36% helix, 22% strand | P10378, Q1REW7 |
| H | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 611 | 35% helix, 23% strand | P10378, Q1REW7 |
| I | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 608 | 35% helix, 22% strand | P10378, Q1REW7 |
| J | Enterobactin synthase component E (ente), 2,3-dihydro-2,3- dihydroxybenzoate synthetase, isochroismatase (entb) (EC 2.7.7.58, 2.3.1.-) | protein | 606 | 36% helix, 21% strand | P10378, Q1REW7 |
Ligands and binding sites
- SVS · 5'-deoxy-5'-({[2-(2-hydroxyphenyl)ethyl]sulfonyl}amino)adenosine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- PNS · 4'-phosphopantetheine · ligand · 10 copies · chains A, B, C, H, D, E, F, I, G, J
- IOD · Iodide ion · ion · 25 copies · chains A, B, C, D, E, F, G, H, I, 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 | 1021 | 0.87 | 0.88 | 116 | PNS, SVS, IOD |
| 2 | 1003 | 0.86 | 0.87 | 124 | SVS, PNS |
| 3 | 1042 | 0.86 | 0.87 | 116 | PNS, SVS |
| 4 | 994 | 0.86 | 0.87 | 105 | SVS, PNS |
| 5 | 1102 | 0.86 | 0.87 | 110 | SVS, IOD, PNS |
Interfaces
20 interfaces between chains.
- F–I · 2265 Ų buried · 16 hydrogen bonds · protein-protein
- C–H · 2243 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1984 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1932 Ų buried · 14 hydrogen bonds · protein-protein
- G–J · 1890 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 cofactor (phosphopantetheinylation).
Compared structures
- 3RG2 · Structure of a two-domain NRPS fusion protein containing the EntE adenylation domain and… · the same entry in another collection · chain J against J, TM-score 1.00
- P10378 · AlphaFold monomer V2.0 prediction for enterobactin synthase component E (P10378) · a predicted model of the same protein · chain F against A, TM-score 0.87
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 P10378
- Every structure of UniProt Q1REW7
- Elsewhere: RCSB PDB 3RG2 · PDBe 3RG2 · UniProt P10378 · UniProt Q1REW7
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