MolNFT v1 · #115989 · protein
Crystal structure of bsha from B. subtilis complexed with N- acetylglucosaminyl-malate and ump
5D00 · N-acetyl-alpha-D-glucosaminyl L-malate synthase: “Crystal structure of bsha from B. subtilis complexed with N- acetylglucosaminyl-malate and ump”. X-ray diffraction, 3 ligands (GMT, U5P, PO4), 3 pockets (best druggability 0.75).…
- PDB
- 5D00
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-alpha-D-glucosaminyl L-malate synthase
- EC
- 2.4.1.-
- UniProt
- P42982
- Ligands
- GMT, U5P, PO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyl-alpha-D-glucosaminyl L-malate synthase (EC 2.4.1.-) | protein | 361 | 48% helix, 17% strand | P42982 |
| B | N-acetyl-alpha-D-glucosaminyl L-malate synthase (EC 2.4.1.-) | protein | 361 | 47% helix, 18% strand | P42982 |
Ligands and binding sites
- GMT · (2S)-2-{[2-acetamido-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid · ligand · 2 copies · chains A, B
- U5P · Uridine-5'-monophosphate · ligand · chains B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.75 | 0.82 | 60 | GMT, PO4 |
| 2 | 606 | 0.74 | 0.81 | 59 | GMT, U5P |
| 3 | 55 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1815 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5D00 · Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate and… · the same entry in another collection · chain A against A, TM-score 1.00
- P42982 · AlphaFold monomer V2.0 prediction for N-acetyl-alpha-D-glucosaminyl L-malate synthase… · a predicted model of the same protein · chain B 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 P42982
- Elsewhere: RCSB PDB 5D00 · PDBe 5D00 · UniProt P42982
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