MolNFT v1 · #56154 · protein
Crystal structure analysis of (GP27-GP5)3 conjugated with FE(III) protoporphyrin
2Z6B · Tail-associated lysozyme: “Crystal structure analysis of (GP27-GP5)3 conjugated with FE(III) protoporphyrin”. X-ray diffraction, 1 ligand (NEN), 15 pockets (best druggability 0.74). MolNFT v1 #56154 on GenesisL1: 3D structure…
- PDB
- 2Z6B
- Type
- protein
- Length
- 941 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail-associated lysozyme; Baseplate structural protein GP27
- EC
- 3.2.1.17
- UniProt
- P16009, P17172
- Ligands
- NEN
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tail-associated lysozyme (EC 3.2.1.17) | protein | 573 | 20% helix, 15% strand | P16009 |
| D | Baseplate structural protein GP27 | protein | 368 | 14% helix, 35% strand | P17172 |
Ligands and binding sites
- NEN · 1-ethyl-pyrrolidine-2,5-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.74 | 0.82 | 65 | empty |
| 2 | 298 | 0.63 | 0.80 | 32 | empty |
| 3 | 66 | 0.58 | 0.89 | 23 | empty |
| 4 | 226 | 0.57 | 0.79 | 27 | empty |
| 5 | 92 | 0.56 | 0.85 | 20 | empty |
Interfaces
1 interface between chains.
- A–D · 1039 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Z6B · Crystal Structure Analysis of (gp27-gp5)3 conjugated with Fe(III) protoporphyrin · 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 P16009
- Every structure of UniProt P17172
- Elsewhere: RCSB PDB 2Z6B · PDBe 2Z6B · UniProt P16009 · UniProt P17172
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