MolNFT v1 · #152945 · protein
The structure of ente with 2-nitrobenzoyl adenylate analog
6IYK · 2,3-dihydroxybenzoate-AMP ligase component of enterobactin…: “The structure of ente with 2-nitrobenzoyl adenylate analog”. X-ray diffraction, 1 ligand (B1U), 9 pockets (best druggability 0.80). MolNFT v1 #152945 on GenesisL1: 3D…
- PDB
- 6IYK
- Type
- protein
- Length
- 1,044 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex
- EC
- 2.7.7.58
- UniProt
- A0A0E1LUI6
- Ligands
- B1U
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex (EC 2.7.7.58) | protein | 521 | 33% helix, 26% strand | A0A0E1LUI6 |
| B | 2,3-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex (EC 2.7.7.58) | protein | 523 | 33% helix, 26% strand | A0A0E1LUI6 |
Ligands and binding sites
- B1U · 5'-O-[(2-nitrobenzene-1-carbonyl)sulfamoyl]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.80 | 0.83 | 120 | B1U |
| 2 | 633 | 0.79 | 0.84 | 98 | B1U |
| 3 | 127 | 0.40 | 0.75 | 22 | empty |
| 4 | 91 | 0.37 | 0.76 | 14 | empty |
| 5 | 72 | 0.36 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 419 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6IYK · The structure of EntE with 2-nitrobenzoyl adenylate analog · 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 A0A0E1LUI6
- Elsewhere: RCSB PDB 6IYK · PDBe 6IYK · UniProt A0A0E1LUI6
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