Research workbench
Mura (ASP305ALA) liganded with tetrahedral reaction intermediate
Analyse Mura (ASP305ALA) liganded with tetrahedral reaction intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q3G
- Type
- protein
- Length
- 6,704 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 1-carboxyvinyltransferase
- EC
- 2.5.1.7
- UniProt
- P33038
- Ligands
- UDA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, W, X, Y, Z | Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) | protein | 419 | 35% helix, 28% strand | P33038 |
Ligands and binding sites
- UDA · 3'-1-carboxy-1-phosphonooxy-ethoxy-uridine-diphosphate-N-acetylglucosamine · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, W, X, Y, Z
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, W, X, Y, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.85 | 0.90 | 79 | UDA, EDO |
| 2 | 560 | 0.84 | 0.90 | 70 | UDA, EDO |
| 3 | 541 | 0.84 | 0.90 | 73 | UDA, EDO |
| 4 | 521 | 0.84 | 0.90 | 59 | UDA, EDO |
| 5 | 503 | 0.84 | 0.90 | 64 | UDA, EDO |
Interfaces
37 interfaces between chains.
- W–X · 1081 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 1068 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1062 Ų buried · 9 hydrogen bonds · protein-protein
- Y–Z · 1056 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1047 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (nonstandard).
Compared structures
- 1Q3G · MurA (Asp305Ala) liganded with tetrahedral reaction intermediate · the same entry in another collection · chain Z against Z, 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
- Every structure of UniProt P33038
- Elsewhere: RCSB PDB 1Q3G · PDBe 1Q3G · UniProt P33038
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