MolNFT v1 · #31314 · protein
E90A mutant structure of plyl
2AR3 · Prophage LAMBDABA02, N-acetylmuramoyl-L-alanine amidase…: “E90A mutant structure of plyl”. X-ray diffraction, 2 ligands (ZN, PO4), 5 pockets (best druggability 0.62). MolNFT v1 #31314 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2AR3
- Type
- protein
- Length
- 473 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prophage LAMBDABA02, N-acetylmuramoyl-L-alanine amidase, family 2
- EC
- 3.5.1.28
- UniProt
- Q81WA9
- Ligands
- ZN, PO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Prophage LAMBDABA02, N-acetylmuramoyl-L-alanine amidase, family 2 (EC 3.5.1.28) | protein | 157 | 41% helix, 17% strand | Q81WA9 |
| B | Prophage LAMBDABA02, N-acetylmuramoyl-L-alanine amidase, family 2 (EC 3.5.1.28) | protein | 159 | 40% helix, 16% strand | Q81WA9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.62 | 0.77 | 51 | ZN, PO4 |
| 2 | 285 | 0.59 | 0.78 | 29 | ZN, PO4 |
| 3 | 268 | 0.59 | 0.79 | 31 | ZN, PO4 |
| 4 | 58 | 0.37 | 0.79 | 15 | empty |
| 5 | 55 | 0.32 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 338 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 335 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2AR3 · E90A mutant structure of PlyL · 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
- Every structure of UniProt Q81WA9
- Elsewhere: RCSB PDB 2AR3 · PDBe 2AR3 · UniProt Q81WA9
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