MolNFT v1 · #176758 · protein
The structure of T4 lysozyme I3C/C54T/R125C/E128C complex with zinc ions
7DWS · Endolysin: “The structure of T4 lysozyme I3C/C54T/R125C/E128C complex with zinc ions”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.67). MolNFT v1 #176758 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7DWS
- Type
- protein
- Length
- 421 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endolysin
- EC
- 3.2.1.17
- UniProt
- D9IEF7
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endolysin (EC 3.2.1.17) | protein | 164 | 59% helix, 6% strand | D9IEF7 |
| B | Endolysin (EC 3.2.1.17) | protein | 133 | 65% helix, 0% strand | D9IEF7 |
| C | Endolysin (EC 3.2.1.17) | protein | 124 | 68% helix, 0% strand | D9IEF7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 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 | 337 | 0.67 | 0.81 | 43 | empty |
| 2 | 188 | 0.60 | 0.82 | 30 | empty |
| 3 | 50 | 0.50 | 0.87 | 13 | empty |
| 4 | 117 | 0.47 | 0.79 | 24 | empty |
| 5 | 72 | 0.28 | 0.72 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 517 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 217 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7DWS · The structure of T4 Lysozyme I3C/C54T/R125C/E128C complex with Zinc ions · 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 D9IEF7
- Elsewhere: RCSB PDB 7DWS · PDBe 7DWS · UniProt D9IEF7
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