MolNFT v1 · #161170 · protein
High resolution electron cryo-microscopy structure of the bacteriophage PR772
6Q5U · Major capsid protein (P3): “High resolution electron cryo-microscopy structure of the bacteriophage PR772”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #161170 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Q5U
- Type
- protein
- Length
- 5,386 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein (P3); Minor capsid protein (P30); Infectivity protein (P16); Spike…
- UniProt
- Q6EDX0, Q6EDW3, Q6EDW1, Q6EDX8, Q6EDY0
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 12 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Major capsid protein (P3) | protein | 390 | 11% helix, 39% strand | Q6EDX0 |
| B, K | Major capsid protein (P3) | protein | 377 | 13% helix, 40% strand | Q6EDX0 |
| C, F, I | Major capsid protein (P3) | protein | 394 | 13% helix, 38% strand | Q6EDX0 |
| D | Major capsid protein (P3) | protein | 380 | 13% helix, 39% strand | Q6EDX0 |
| E | Major capsid protein (P3) | protein | 379 | 13% helix, 41% strand | Q6EDX0 |
| G | Major capsid protein (P3) | protein | 388 | 14% helix, 41% strand | Q6EDX0 |
| H | Major capsid protein (P3) | protein | 374 | 13% helix, 40% strand | Q6EDX0 |
| L | Major capsid protein (P3) | protein | 392 | 15% helix, 40% strand | Q6EDX0 |
| M | Minor capsid protein (P30) | protein | 84 | 5% helix, 8% strand | Q6EDW3 |
| N | Infectivity protein (P16) | protein | 51 | 37% helix, 2% strand | Q6EDW1 |
| O, P, Q | Spike protein | protein | 124 | 4% helix, 35% strand | Q6EDX8 |
| R, S | Penton protein | protein | 125 | 5% helix, 29% strand | Q6EDY0 |
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 | 1172 | 0.89 | 0.91 | 165 | empty |
| 2 | 759 | 0.87 | 0.90 | 117 | empty |
| 3 | 1034 | 0.79 | 0.80 | 120 | empty |
| 4 | 408 | 0.77 | 0.86 | 42 | empty |
| 5 | 1084 | 0.77 | 0.79 | 107 | empty |
Interfaces
39 interfaces between chains.
- J–K · 2110 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 2071 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2067 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2053 Ų buried · 31 hydrogen bonds · protein-protein
- G–I · 2048 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6Q5U · High resolution electron cryo-microscopy structure of the bacteriophage PR772 · 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 Q6EDX0
- Every structure of UniProt Q6EDW3
- Every structure of UniProt Q6EDW1
- Every structure of UniProt Q6EDX8
- Every structure of UniProt Q6EDY0
- Elsewhere: RCSB PDB 6Q5U · PDBe 6Q5U · UniProt Q6EDX0 · UniProt Q6EDW3 · UniProt Q6EDW1 · UniProt Q6EDX8 · UniProt Q6EDY0
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