Research workbench
Crystal structure of udp-N-acetylmuramic ACID:L-alanine ligase (murc) in complex with uma and anp.
Analyse Crystal structure of udp-N-acetylmuramic ACID:L-alanine ligase (murc) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P3D
- Type
- protein
- Length
- 923 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramate--alanine ligase
- EC
- 6.3.2.8
- UniProt
- P45066
- Ligands
- UMA, ANP, MN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramate--alanine ligase (EC 6.3.2.8) | protein | 463 | 37% helix, 26% strand | P45066 |
| B | Udp-N-acetylmuramate--alanine ligase (EC 6.3.2.8) | protein | 460 | 36% helix, 26% strand | P45066 |
Ligands and binding sites
- UMA · Uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine · ligand · 2 copies · chains A, B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
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 | 1027 | 0.80 | 0.81 | 112 | MN, UMA, ANP |
| 2 | 1183 | 0.77 | 0.79 | 112 | MN, UMA, ANP |
| 3 | 114 | 0.50 | 0.81 | 19 | empty |
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 1P3D · Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA… · the same entry in another collection · chain A against A, TM-score 1.00
- P45066 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramate--L-alanine ligase (P45066) · 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 P45066
- Elsewhere: RCSB PDB 1P3D · PDBe 1P3D · UniProt P45066
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