Research workbench
2.25 ångström resolution crystal structure of udp-N-acetylmuramate--L- alanine ligase (murc) from yersinia pestis CO92 in complex with AMP
Analyse 2.25 ångström resolution crystal structure of udp-N-acetylmuramate--L- alanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HV4
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramate--L-alanine ligase
- EC
- 6.3.2.8
- UniProt
- Q8ZIE8
- Ligands
- AMP
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) | protein | 465 | 36% helix, 25% strand | Q8ZIE8 |
| B | Udp-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) | protein | 462 | 38% helix, 25% strand | Q8ZIE8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.79 | 0.83 | 99 | AMP |
| 2 | 575 | 0.78 | 0.84 | 78 | AMP |
| 3 | 312 | 0.59 | 0.77 | 30 | empty |
| 4 | 265 | 0.58 | 0.78 | 35 | empty |
| 5 | 79 | 0.42 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 855 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4HV4 · 2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZIE8 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramate--L-alanine ligase (Q8ZIE8) · 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 Q8ZIE8
- Elsewhere: RCSB PDB 4HV4 · PDBe 4HV4 · UniProt Q8ZIE8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.