Research workbench
Fitting of GP11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex
Analyse Fitting of GP11 crystal structure into 3D cryo-EM reconstruction of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PDF
- Type
- protein
- Length
- 3,744 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate structural protein GP11
- UniProt
- P10929
- Pockets
- 6 · best druggability 0.38
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 GP11 | protein | 208 | 0% helix, 0% strand | P10929 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.38 | 0.73 | 26 | empty |
| 2 | 99 | 0.36 | 0.73 | 23 | empty |
| 3 | 79 | 0.33 | 0.73 | 19 | empty |
| 4 | 66 | 0.32 | 0.73 | 20 | empty |
| 5 | 64 | 0.30 | 0.73 | 23 | empty |
Interfaces
18 interfaces between chains.
- P–Q · 326 Ų buried · 0 hydrogen bonds · protein-protein
- G–H · 325 Ų buried · 0 hydrogen bonds · protein-protein
- J–K · 325 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 325 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 325 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PDF · Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4… · 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 P10929
- Elsewhere: RCSB PDB 1PDF · PDBe 1PDF · UniProt P10929
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