MolNFT v1 · #91311 · protein
Structure of escherichia COLI pgab 42-655 in complex with iron
4F9J · Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase: “Structure of escherichia COLI pgab 42-655 in complex with iron”. X-ray diffraction, 2 ligands (FE, CA), 13 pockets (best druggability 0.70). MolNFT v1 #91311 on GenesisL1: 3D…
- PDB
- 4F9J
- Type
- protein
- Length
- 1,198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
- EC
- 3.5.1.-
- UniProt
- P75906
- Ligands
- FE, CA
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase (EC 3.5.1.-) | protein | 599 | 45% helix, 19% strand | P75906 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.70 | 0.75 | 102 | empty |
| 2 | 556 | 0.64 | 0.75 | 56 | empty |
| 3 | 405 | 0.59 | 0.75 | 45 | empty |
| 4 | 310 | 0.57 | 0.76 | 44 | MES |
| 5 | 90 | 0.53 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4F9J · Structure of Escherichia coli PgaB 42-655 in complex with iron · the same entry in another collection · chain A against A, TM-score 1.00
- P75906 · AlphaFold monomer V2.0 prediction for poly-beta-1,6-N-acetyl-D- glucosamine N-deacetylase… · 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 P75906
- Elsewhere: RCSB PDB 4F9J · PDBe 4F9J · UniProt P75906
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