MolNFT v1 · #59561 · protein
Crystal structure of an antioxidant defense protein (MLR4105) from mesorhizobium loti MAFF303099 at 2.00 a resolution
3C1L · Putative antioxidant defense protein MLR4105: “Crystal structure of an antioxidant defense protein (MLR4105) from mesorhizobium loti MAFF303099 at 2.00 a…”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.83).…
- PDB
- 3C1L
- Type
- protein
- Length
- 2,183 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative antioxidant defense protein MLR4105
- UniProt
- Q98ES4
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative antioxidant defense protein MLR4105 | protein | 182 | 73% helix, 0% strand | Q98ES4 |
| B | Putative antioxidant defense protein MLR4105 | protein | 185 | 70% helix, 0% strand | Q98ES4 |
| C, J | Putative antioxidant defense protein MLR4105 | protein | 183 | 73% helix, 0% strand | Q98ES4 |
| D | Putative antioxidant defense protein MLR4105 | protein | 180 | 73% helix, 0% strand | Q98ES4 |
| E, F | Putative antioxidant defense protein MLR4105 | protein | 181 | 74% helix, 0% strand | Q98ES4 |
| G | Putative antioxidant defense protein MLR4105 | protein | 185 | 71% helix, 0% strand | Q98ES4 |
| H | Putative antioxidant defense protein MLR4105 | protein | 180 | 74% helix, 0% strand | Q98ES4 |
| I, K, L | Putative antioxidant defense protein MLR4105 | protein | 181 | 72% helix, 0% strand | Q98ES4 |
Ligands and binding sites
- CL · Chloride ion · ion · chains J
- PEG · Di(hydroxyethyl)ether · additive · 25 copies · chains A, G, B, C, D, E, H, I, J
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 | 893 | 0.83 | 0.85 | 100 | PEG |
| 2 | 902 | 0.83 | 0.85 | 102 | PEG |
| 3 | 967 | 0.83 | 0.84 | 109 | empty |
| 4 | 810 | 0.81 | 0.83 | 94 | PEG |
| 5 | 1139 | 0.78 | 0.80 | 109 | PEG |
Interfaces
26 interfaces between chains.
- A–B · 1908 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1878 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1868 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1802 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1745 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 97 modified (engineered).
Compared structures
- 3C1L · Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti… · 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 Q98ES4
- Elsewhere: RCSB PDB 3C1L · PDBe 3C1L · UniProt Q98ES4
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