MolNFT v1 · #116150 · protein
Crystal structure of repressor from salmonella-temperate phage
5D4Z: “Crystal structure of repressor from salmonella-temperate phage”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #116150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D4Z
- Type
- protein
- Length
- 3,313 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Repressor
- UniProt
- T1S9Z0
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 53% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, I, K, L, M, O, Q, R, T, V, W, X, Y, 1, 7 | Repressor | protein | 105 | 58% helix, 1% strand | T1S9Z0 |
| D, 2, 6 | Repressor | protein | 101 | 60% helix, 1% strand | T1S9Z0 |
| H, N | Repressor | protein | 102 | 56% helix, 1% strand | T1S9Z0 |
| J, U | Repressor | protein | 103 | 51% helix, 0% strand | T1S9Z0 |
| P, Z, 3, 4, 5 | Repressor | protein | 100 | 37% helix, 1% strand | T1S9Z0 |
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 | 693 | 0.85 | 0.89 | 75 | empty |
| 2 | 868 | 0.83 | 0.86 | 109 | empty |
| 3 | 1097 | 0.83 | 0.84 | 106 | empty |
| 4 | 971 | 0.81 | 0.83 | 76 | empty |
| 5 | 1157 | 0.81 | 0.82 | 116 | empty |
Interfaces
78 interfaces between chains.
- Q–R · 1964 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 1957 Ų buried · 15 hydrogen bonds · protein-protein
- X–Y · 1863 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1862 Ų buried · 14 hydrogen bonds · protein-protein
- T–U · 1830 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5D4Z · Crystal structure of Repressor from Salmonella-temperate phage · the same entry in another collection · chain B against B, 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 T1S9Z0
- Elsewhere: RCSB PDB 5D4Z · PDBe 5D4Z · UniProt T1S9Z0
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