Research workbench
Crystal structure of reduced tryparedoxin peroxidase from leishmania major at 2.34 a resolution
Analyse Crystal structure of reduced tryparedoxin peroxidase from leishmania major at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K1F
- Type
- protein
- Length
- 987 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryparedoxin peroxidase
- EC
- 1.11.1.15
- UniProt
- Q4QF76
- Ligands
- CL
- Pockets
- 11 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Tryparedoxin peroxidase (EC 1.11.1.15) | protein | 198 | 31% helix, 26% strand | Q4QF76 |
| D | Tryparedoxin peroxidase (EC 1.11.1.15) | protein | 196 | 31% helix, 25% strand | Q4QF76 |
| E | Tryparedoxin peroxidase (EC 1.11.1.15) | protein | 197 | 31% helix, 25% strand | Q4QF76 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, C, D, E
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D, E
- PGE · Triethylene glycol · additive · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.53 | 0.79 | 34 | empty |
| 2 | 213 | 0.52 | 0.76 | 23 | PEG |
| 3 | 216 | 0.51 | 0.76 | 23 | PEG |
| 4 | 159 | 0.49 | 0.77 | 22 | PEG |
| 5 | 114 | 0.46 | 0.79 | 21 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2091 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2084 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 790 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 772 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4K1F · Crystal structure of reduced tryparedoxin peroxidase from leishmania major at 2.34 A… · 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 Q4QF76
- Elsewhere: RCSB PDB 4K1F · PDBe 4K1F · UniProt Q4QF76
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