MolNFT v1 · #174436 · protein
Crystal structure of udp-N-acetylmuramic acid L-alanine ligase (murc) from mycobacterium bovis in complex with udp-N-acetylglucosamine
7BVB · Udp-N-acetylmuramate--L-alanine ligase: “Crystal structure of udp-N-acetylmuramic acid L-alanine ligase (murc) from mycobacterium bovis in complex…”. X-ray diffraction, 2 ligands (UD1, ZN), 9 pockets (best druggability 0.78). MolNFT…
- PDB
- 7BVB
- Type
- protein
- Length
- 938 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
- P65473
- Ligands
- UD1, ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) | protein | 475 | 36% helix, 23% strand | P65473 |
| B | Udp-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) | protein | 463 | 37% helix, 24% strand | P65473 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.78 | 0.84 | 62 | empty |
| 2 | 484 | 0.77 | 0.85 | 58 | empty |
| 3 | 537 | 0.66 | 0.77 | 46 | UD1 |
| 4 | 394 | 0.61 | 0.77 | 37 | UD1, ZN |
| 5 | 180 | 0.60 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1018 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7BVB · Crystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- P65473 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramate--L-alanine ligase (P65473) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P65473
- Elsewhere: RCSB PDB 7BVB · PDBe 7BVB · UniProt P65473
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