Research workbench
Fitting of the GP9 structure in the EM density of bacteriophage T4 extended tail
Analyse Fitting of the GP9 structure in the EM density of bacteriophage T4 extended tail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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