MolNFT v1 · #137369 · protein
Crystal structure of a bifunctional glmu udp-N-acetylglucosamine DIPHOSPHORYLASE/GLUCOSAMINE-1- phosphate N-acetyltransferase from acinetobacter baumannii
5VMK · Bifunctional protein glmu: “Crystal structure of a bifunctional glmu udp-N-acetylglucosamine DIPHOSPHORYLASE/GLUCOSAMINE-1- phosphate…”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.76). MolNFT v1 #137369 on…
- PDB
- 5VMK
- Type
- protein
- Length
- 1,294 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein glmu
- EC
- 2.3.1.157, 2.7.7.23
- UniProt
- A0A0D5YCC7
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein glmu (EC 2.3.1.157, 2.7.7.23) | protein | 449 | 20% helix, 33% strand | A0A0D5YCC7 |
| B | Bifunctional protein glmu (EC 2.3.1.157, 2.7.7.23) | protein | 430 | 21% helix, 34% strand | A0A0D5YCC7 |
| C | Bifunctional protein glmu (EC 2.3.1.157, 2.7.7.23) | protein | 415 | 19% helix, 33% strand | A0A0D5YCC7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
- CIT · Citric acid · additive · 3 copies · chains A, C, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.76 | 0.80 | 86 | CIT, PG4 |
| 2 | 702 | 0.74 | 0.80 | 83 | CIT, PG4 |
| 3 | 558 | 0.72 | 0.81 | 77 | CIT |
| 4 | 148 | 0.70 | 0.89 | 29 | empty |
| 5 | 385 | 0.69 | 0.81 | 34 | PG4 |
Interfaces
3 interfaces between chains.
- B–C · 2262 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2221 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2188 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5VMK · Crystal structure of a bifunctional GlmU UDP-N-acetylglucosamine… · 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
- Every structure of UniProt A0A0D5YCC7
- Elsewhere: RCSB PDB 5VMK · PDBe 5VMK · UniProt A0A0D5YCC7
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