Research workbench
Sp protein ligand 1
Analyse Sp protein ligand 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AM1
- Type
- protein
- Length
- 454 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D- alanine ligase, murf protein
- EC
- 6.3.2.10
- Ligands
- 1LG
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D- alanine ligase, murf protein (EC 6.3.2.10) | protein | 454 | 35% helix, 20% strand | — |
Ligands and binding sites
- 1LG · 2,4-dichloro-N-(3-cyano-4,5,6,7-tetrahydro-benzothiophen-2YL)-5-(morpholine-4-sulfonyl)-benzamide · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.81 | 0.82 | 99 | 1LG, GOL |
| 2 | 76 | 0.43 | 0.80 | 17 | empty |
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2AM1 · sp protein ligand 1 · 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
- Elsewhere: RCSB PDB 2AM1 · PDBe 2AM1
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