MolNFT v2 · #228965 · protein
Structure of the urea-treated empty bacteriophage T5 portal complex
9IMV · Portal protein pb7: “Structure of the urea-treated empty bacteriophage T5 portal complex”. Electron microscopy at 4.0, 20 pockets (best druggability 0.86). MolNFT v2 #228965 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 9IMV
- Type
- protein
- Length
- 6,480 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.0
- Source
- Escherichia phage T5
- Molecule
- Portal protein pb7; Head completion protein
- UniProt
- Q6QGD5, Q6QGD9
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 4.0 · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Portal protein pb7 | protein | 370 | 43% helix, 13% strand | Q6QGD5 |
| M, N, O, P, Q, R, S, T, U, V, W, X | Head completion protein | protein | 170 | 31% helix, 28% strand | Q6QGD9 |
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 | 948 | 0.86 | 0.87 | 120 | empty |
| 2 | 931 | 0.86 | 0.87 | 112 | empty |
| 3 | 1138 | 0.83 | 0.84 | 137 | empty |
| 4 | 1011 | 0.83 | 0.84 | 115 | empty |
| 5 | 1158 | 0.82 | 0.83 | 136 | empty |
Interfaces
77 interfaces between chains.
- E–F · 5489 Ų buried · 68 hydrogen bonds · protein-protein
- H–I · 5470 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 5454 Ų buried · 75 hydrogen bonds · protein-protein
- F–G · 5452 Ų buried · 69 hydrogen bonds · protein-protein
- J–K · 5443 Ų buried · 68 hydrogen bonds · protein-protein
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 Q6QGD5
- Every structure of UniProt Q6QGD9
- Elsewhere: RCSB PDB 9IMV · PDBe 9IMV · UniProt Q6QGD5 · UniProt Q6QGD9
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