MolNFT v1 · #170668 · protein
Crystal structure of msra C206 and trx C35S complex from escherichia COLI
6YEV · Thioredoxin 1: “Crystal structure of msra C206 and trx C35S complex from escherichia COLI”. X-ray diffraction, 1 ligand (NA), 14 pockets (best druggability 0.75). MolNFT v1 #170668 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YEV
- Type
- protein
- Length
- 1,142 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin 1; Peptide methionine sulfoxide reductase msra
- EC
- 1.8.4.11
- UniProt
- P0AA25, P0A744
- Ligands
- NA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Thioredoxin 1 | protein | 103 | 27% helix, 28% strand | P0AA25 |
| F | Thioredoxin 1 | protein | 108 | 35% helix, 27% strand | P0AA25 |
| A | Peptide methionine sulfoxide reductase msra (EC 1.8.4.11) | protein | 209 | 26% helix, 18% strand | P0A744 |
| B | Peptide methionine sulfoxide reductase msra (EC 1.8.4.11) | protein | 207 | 28% helix, 19% strand | P0A744 |
| C | Peptide methionine sulfoxide reductase msra (EC 1.8.4.11) | protein | 208 | 28% helix, 19% strand | P0A744 |
| D | Peptide methionine sulfoxide reductase msra (EC 1.8.4.11) | protein | 201 | 27% helix, 19% strand | P0A744 |
| G | Thioredoxin 1 | protein | 106 | 27% helix, 22% strand | P0AA25 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.75 | 0.78 | 110 | empty |
| 2 | 801 | 0.72 | 0.77 | 94 | empty |
| 3 | 511 | 0.64 | 0.76 | 56 | empty |
| 4 | 77 | 0.56 | 0.86 | 18 | empty |
| 5 | 82 | 0.50 | 0.83 | 23 | empty |
Interfaces
11 interfaces between chains.
- C–G · 538 Ų buried · 3 hydrogen bonds · protein-protein
- E–A · 515 Ų buried · 5 hydrogen bonds · protein-protein
- F–B · 483 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 474 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6YEV · Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli · the same entry in another collection · chain G against G, TM-score 1.00
- P0A744 · AlphaFold monomer V2.0 prediction for peptide methionine sulfoxide reductase msra (P0A744) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P0AA25
- Every structure of UniProt P0A744
- Elsewhere: RCSB PDB 6YEV · PDBe 6YEV · UniProt P0AA25 · UniProt P0A744
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