Research workbench
Crystal structure of NADP-bound wbjb from a. baumannii community strain D1279779
Analyse Crystal structure of NADP-bound wbjb from a. baumannii community strain D1279779 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J2O
- Type
- protein
- Length
- 1,859 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 4,6-DEHYDRATASE/5-epimerase
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 4,6-DEHYDRATASE/5-epimerase | protein | 315 | 41% helix, 20% strand | — |
| B | Udp-N-acetylglucosamine 4,6-DEHYDRATASE/5-epimerase | protein | 313 | 41% helix, 20% strand | — |
| C | Udp-N-acetylglucosamine 4,6-DEHYDRATASE/5-epimerase | protein | 316 | 41% helix, 20% strand | — |
| D | Udp-N-acetylglucosamine 4,6-DEHYDRATASE/5-epimerase | protein | 312 | 42% helix, 20% strand | — |
| E | Udp-N-acetylglucosamine 4,6-DEHYDRATASE/5-epimerase | protein | 303 | 42% helix, 19% strand | — |
| F | Udp-N-acetylglucosamine 4,6-DEHYDRATASE/5-epimerase | protein | 300 | 42% helix, 19% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.83 | 0.85 | 91 | NAP |
| 2 | 873 | 0.82 | 0.84 | 80 | NAP |
| 3 | 651 | 0.81 | 0.86 | 69 | NAP |
| 4 | 1006 | 0.81 | 0.82 | 88 | NAP |
| 5 | 868 | 0.79 | 0.82 | 85 | NAP |
Interfaces
12 interfaces between chains.
- B–F · 1113 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1078 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1074 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1042 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 955 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 81 modified (engineered).
Compared structures
- 4J2O · Crystal structure of NADP-bound WbjB from A. baumannii community strain D1279779 · 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
- Elsewhere: RCSB PDB 4J2O · PDBe 4J2O
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