Research workbench
Fitting of GP9 structure into the bacteriophage T4 baseplate cryoem reconstruction
Analyse Fitting of GP9 structure into the bacteriophage T4 baseplate cryoem… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PDP
- 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
- 7 · best druggability 0.32
Structure
electron microscopy · 1 distinct chain · 0% helix, 0% 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 | 0% helix, 0% strand | P10927 |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.32 | 0.72 | 19 | empty |
| 2 | 54 | 0.28 | 0.72 | 15 | empty |
| 3 | 50 | 0.28 | 0.73 | 17 | empty |
| 4 | 50 | 0.27 | 0.73 | 16 | empty |
| 5 | 53 | 0.27 | 0.72 | 17 | empty |
Interfaces
18 interfaces between chains.
- J–K · 382 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 381 Ų buried · 0 hydrogen bonds · protein-protein
- P–Q · 381 Ų buried · 0 hydrogen bonds · protein-protein
- G–H · 381 Ų buried · 0 hydrogen bonds · protein-protein
- P–R · 381 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PDP · Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction · 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 1PDP · PDBe 1PDP · UniProt P10927
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