Research workbench
Structure of escherichia COLI pgab 42-655 in complex with nickel
Analyse Structure of escherichia COLI pgab 42-655 in complex with nickel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F9D
- Type
- protein
- Length
- 1,184 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
- NI, CA
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 44% 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 | 592 | 44% helix, 19% strand | P75906 |
Ligands and binding sites
- NI · Nickel (II) 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
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.71 | 0.75 | 88 | empty |
| 2 | 717 | 0.68 | 0.76 | 70 | NI, ACY |
| 3 | 333 | 0.57 | 0.76 | 49 | MES |
| 4 | 78 | 0.56 | 0.87 | 19 | empty |
| 5 | 290 | 0.55 | 0.76 | 42 | MES |
Interfaces
1 interface between chains.
- A–B · 1140 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4F9D · Structure of Escherichia coli PgaB 42-655 in complex with nickel · 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 4F9D · PDBe 4F9D · UniProt P75906
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