MolNFT v1 · #181057 · protein
Human PRX1-srx decameric complex
7LJ1 · Peroxiredoxin-1: “Human PRX1-srx decameric complex”. X-ray diffraction, 2 ligands (ATP, PO4), 20 pockets (best druggability 0.82). MolNFT v1 #181057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LJ1
- Type
- protein
- Length
- 5,782 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin-1; Sulfiredoxin-1
- EC
- 1.11.1.24, 1.8.98.2
- UniProt
- Q06830, Q9BYN0
- Ligands
- ATP, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 21 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, N, S, T | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 185 | 29% helix, 25% strand | Q06830 |
| a | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 106 | 34% helix, 26% strand | Q9BYN0 |
| C, O | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 187 | 28% helix, 25% strand | Q06830 |
| D | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 181 | 28% helix, 25% strand | Q06830 |
| F | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 185 | 29% helix, 25% strand | Q06830 |
| G | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 182 | 27% helix, 25% strand | Q06830 |
| H, K, P | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 183 | 29% helix, 25% strand | Q06830 |
| I | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 191 | 28% helix, 24% strand | Q06830 |
| J | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 184 | 27% helix, 25% strand | Q06830 |
| L | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 181 | 28% helix, 25% strand | Q06830 |
| M | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 178 | 28% helix, 25% strand | Q06830 |
| Q | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 184 | 29% helix, 25% strand | Q06830 |
| R | Peroxiredoxin-1 (EC 1.11.1.24) | protein | 186 | 28% helix, 25% strand | Q06830 |
| b, c, e, j, m, o, q, s, t | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 107 | 34% helix, 25% strand | Q9BYN0 |
| d, h, p | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 108 | 36% helix, 25% strand | Q9BYN0 |
| f | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 106 | 34% helix, 25% strand | Q9BYN0 |
| g | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 102 | 38% helix, 27% strand | Q9BYN0 |
| i, l | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 103 | 35% helix, 27% strand | Q9BYN0 |
| k | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 97 | 37% helix, 28% strand | Q9BYN0 |
| n | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 94 | 31% helix, 30% strand | Q9BYN0 |
| r | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 99 | 36% helix, 27% strand | Q9BYN0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, c, G, g
- PO4 · Phosphate ion · ion · 19 copies · chains A, a, E, F, B, b, d, e, f, H, h, I, i, J, j, K, k, L, l, M, m, N, n, O, o, P, p, Q, q, R, r, S, s, T, t
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, b, C, d, h, G, H, g, J, i, O, P, S, Q, R, m
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains D, c, G, J, j, K, l, N, m, O, p, P, s, Q, r, R, q
- GOL · Glycerol · additive · 2 copies · chains G, H, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 899 | 0.82 | 0.84 | 112 | PO4 |
| 2 | 1175 | 0.79 | 0.80 | 122 | PO4 |
| 3 | 591 | 0.77 | 0.83 | 70 | PO4 |
| 4 | 659 | 0.77 | 0.82 | 68 | PO4 |
| 5 | 589 | 0.77 | 0.83 | 59 | EDO, PO4 |
Interfaces
86 interfaces between chains.
- C–D · 1102 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 1051 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1041 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1034 Ų buried · 18 hydrogen bonds · protein-protein
- S–T · 1031 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 7LJ1 · Human Prx1-Srx Decameric Complex · the same entry in another collection · chain I against I, 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 Q06830
- Every structure of UniProt Q9BYN0
- Elsewhere: RCSB PDB 7LJ1 · PDBe 7LJ1 · UniProt Q06830 · UniProt Q9BYN0
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