MolNFT v1 · #29834 · protein
Fitting of the GP9 structure in the EM density of bacteriophage T4 extended tail
1ZKU · Baseplate structural protein GP9: “Fitting of the GP9 structure in the EM density of bacteriophage T4 extended tail”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #29834 on GenesisL1: 3D structure, binding…
- PDB
- 1ZKU
- Type
- protein
- Length
- 5,184 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate structural protein GP9
- UniProt
- P10927
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R | Baseplate structural protein GP9 | protein | 288 | 12% helix, 40% strand | P10927 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.84 | 0.90 | 49 | empty |
| 2 | 532 | 0.84 | 0.90 | 49 | empty |
| 3 | 549 | 0.84 | 0.90 | 48 | empty |
| 4 | 483 | 0.83 | 0.90 | 58 | empty |
| 5 | 489 | 0.83 | 0.90 | 56 | empty |
Interfaces
18 interfaces between chains.
- M–O · 2980 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2979 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2978 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2977 Ų buried · 38 hydrogen bonds · protein-protein
- H–I · 2977 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 1ZKU · Fitting of the gp9 structure in the EM density of bacteriophage T4 extended tail · 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 P10927
- Elsewhere: RCSB PDB 1ZKU · PDBe 1ZKU · UniProt P10927
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.