Research workbench
Crystal structure of P. aeruginosa murb in complex with NADP+
Analyse Crystal structure of P. aeruginosa murb in complex with NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JAY
- Type
- protein
- Length
- 1,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylenolpyruvoylglucosamine reductase
- EC
- 1.1.1.158
- UniProt
- Q9HZM7
- Ligands
- FAD, NAP, K
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Udp-N-acetylenolpyruvoylglucosamine reductase (EC 1.1.1.158) | protein | 338 | 30% helix, 29% strand | Q9HZM7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.84 | 0.88 | 73 | FAD, NAP |
| 2 | 581 | 0.84 | 0.89 | 65 | FAD, NAP |
| 3 | 1006 | 0.82 | 0.83 | 87 | FAD, NAP |
| 4 | 1176 | 0.81 | 0.82 | 94 | FAD, NAP, B3P |
| 5 | 192 | 0.65 | 0.85 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1512 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 84 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4JAY · Crystal structure of P. aeruginosa MurB in complex with NADP+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HZM7 · AlphaFold monomer V2.0 prediction for udp-N- acetylenolpyruvoylglucosamine reductase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9HZM7
- Elsewhere: RCSB PDB 4JAY · PDBe 4JAY · UniProt Q9HZM7
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