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1.3 ångström resolution crystal structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase from streptococcus pneumoniae in complex with (2R)-2-(PHOSPHONOOXY)PROPANOIC acid.
Analyse 1.3 ångström resolution crystal structure of udp-N-acetylglucosamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NKJ
- Type
- protein
- Length
- 842 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 1-carboxyvinyltransferase 1
- EC
- 2.5.1.7
- UniProt
- Q97NQ4
- Ligands
- 0V5, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-N-acetylglucosamine 1-carboxyvinyltransferase 1 (EC 2.5.1.7) | protein | 421 | 35% helix, 28% strand | Q97NQ4 |
Ligands and binding sites
- 0V5 · (2R)-2-(phosphonooxy)propanoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.83 | 0.87 | 67 | 0V5, CIT |
| 2 | 640 | 0.82 | 0.87 | 66 | 0V5, CIT |
| 3 | 121 | 0.56 | 0.84 | 29 | empty |
| 4 | 84 | 0.44 | 0.80 | 29 | empty |
| 5 | 71 | 0.44 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1387 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6NKJ · 1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97NQ4 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 1-carboxyvinyltransferase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q97NQ4
- Elsewhere: RCSB PDB 6NKJ · PDBe 6NKJ · UniProt Q97NQ4
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