MolNFT v1 · #121487 · protein
In vitro assembled star-shaped hubless T4 baseplate
5HX2 · Baseplate wedge protein GP7: “In vitro assembled star-shaped hubless T4 baseplate”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #121487 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HX2
- Type
- protein
- Length
- 4,189 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate wedge protein GP7; Baseplate wedge protein GP8; Baseplate wedge protein GP6…
- UniProt
- P19061, P19062, P19060, P16011, P10928
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 14% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baseplate wedge protein GP7 | protein | 1030 | 10% helix, 15% strand | P19061 |
| B | Baseplate wedge protein GP8 | protein | 334 | 10% helix, 13% strand | P19062 |
| C | Baseplate wedge protein GP8 | protein | 332 | 14% helix, 15% strand | P19062 |
| D | Baseplate wedge protein GP6 | protein | 647 | 17% helix, 11% strand | P19060 |
| E | Baseplate wedge protein GP6 | protein | 634 | 18% helix, 16% strand | P19060 |
| F | Baseplate wedge protein GP53 | protein | 192 | 25% helix, 5% strand | P16011 |
| G, H, I | Baseplate wedge protein GP10 | protein | 340 | 6% helix, 12% strand | P10928 |
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 | 1103 | 0.86 | 0.87 | 166 | empty |
| 2 | 986 | 0.82 | 0.83 | 129 | empty |
| 3 | 715 | 0.81 | 0.85 | 88 | empty |
| 4 | 663 | 0.79 | 0.84 | 89 | empty |
| 5 | 1111 | 0.79 | 0.81 | 99 | empty |
Interfaces
18 interfaces between chains.
- G–I · 2993 Ų buried · 42 hydrogen bonds · protein-protein
- H–I · 2699 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2645 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2583 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2486 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5HX2 · In vitro assembled star-shaped hubless T4 baseplate · 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 P19061
- Every structure of UniProt P19062
- Every structure of UniProt P19060
- Every structure of UniProt P16011
- Every structure of UniProt P10928
- Elsewhere: RCSB PDB 5HX2 · PDBe 5HX2 · UniProt P19061 · UniProt P19062 · UniProt P19060 · UniProt P16011 · UniProt P10928
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