MolNFT v1 · #54863 · protein
Crystal structure of ampd holoenzyme
2Y2D · 1,6-anhydro-N-acetylmuramyl-L-alanine amidase ampd: “Crystal structure of ampd holoenzyme”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.55). MolNFT v1 #54863 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2Y2D
- Type
- protein
- Length
- 537 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,6-anhydro-N-acetylmuramyl-L-alanine amidase ampd
- EC
- 3.5.1.28
- UniProt
- P82974
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 1,6-anhydro-N-acetylmuramyl-L-alanine amidase ampd (EC 3.5.1.28) | protein | 179 | 22% helix, 22% strand | P82974 |
Ligands and binding sites
- ZN · Zinc ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.55 | 0.83 | 34 | empty |
| 2 | 205 | 0.53 | 0.78 | 28 | empty |
| 3 | 209 | 0.51 | 0.76 | 26 | empty |
| 4 | 181 | 0.51 | 0.77 | 29 | empty |
| 5 | 110 | 0.42 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 267 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P82974
- Elsewhere: RCSB PDB 2Y2D · PDBe 2Y2D · UniProt P82974
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