MolNFT v1 · #128298 · protein
Crystal structure of burkholderia AP3 phage endolysin
5NM7 · Peptidoglycan-binding domain 1: “Crystal structure of burkholderia AP3 phage endolysin”. X-ray diffraction, 1 ligand (GLY), 3 pockets (best druggability 0.72). MolNFT v1 #128298 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5NM7
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan-binding domain 1
- Ligands
- GLY
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Peptidoglycan-binding domain 1 | protein | 260 | 55% helix, 5% strand | — |
| A | Peptidoglycan-binding domain 1 | protein | 259 | 59% helix, 5% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.72 | 0.76 | 89 | empty |
| 2 | 222 | 0.59 | 0.80 | 42 | GLY |
| 3 | 149 | 0.56 | 0.82 | 24 | GLY |
Interfaces
1 interface between chains.
- G–A · 607 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NM7 · Crystal structure of Burkholderia AP3 phage endolysin · the same entry in another collection · chain G against G, 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 5NM7 · PDBe 5NM7
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