MolNFT v1 · #78511 · protein
Zn-mediated trimer of T4 lysozyme R125C/E128C by synthetic symmetrization
3SB5: “Zn-mediated trimer of T4 lysozyme R125C/E128C by synthetic symmetrization”. X-ray diffraction, 3 ligands (ZN, MG, CL), 6 pockets (best druggability 0.67). MolNFT v1 #78511 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3SB5
- Type
- protein
- Length
- 654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- ZN, MG, CL
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Lysozyme (EC 3.2.1.17) | protein | 163 | 63% helix, 7% strand | P00720 |
| A, C | Lysozyme (EC 3.2.1.17) | protein | 164 | 61% helix, 9% strand | P00720 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains B, A, C, D
- MG · Magnesium ion · metal · 6 copies · chains B, A, D
- CL · Chloride ion · ion · 8 copies · chains B, A, C, D
- GOL · Glycerol · additive · 9 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.67 | 0.76 | 41 | MG |
| 2 | 556 | 0.66 | 0.76 | 41 | GOL |
| 3 | 183 | 0.44 | 0.74 | 20 | MG |
| 4 | 77 | 0.36 | 0.77 | 26 | empty |
| 5 | 73 | 0.31 | 0.73 | 12 | GOL |
Interfaces
3 interfaces between chains.
- A–D · 417 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 406 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SB5 · Zn-mediated Trimer of T4 Lysozyme R125C/E128C by Synthetic Symmetrization · the same entry in another collection · chain B against B, 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 P00720
- Elsewhere: RCSB PDB 3SB5 · PDBe 3SB5 · UniProt P00720
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