Research workbench
Crystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158L covalently linked with [RH(CP-MAL)(COD)] (NB4-rh) from arabidopsis thaliana
Analyse Crystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158L covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WJC
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0678 fatty acid-binding protein-like protein AT1G79260
- UniProt
- O64527
- Ligands
- RMD, BA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | UPF0678 fatty acid-binding protein-like protein AT1G79260 | protein | 153 | 0% helix, 64% strand | O64527 |
Ligands and binding sites
- RMD · [(1,2,5,6-eta)-cyclooctane-1,2,5,6-tetrayl]{(1,2,3,4,5-eta)-1-[2-(2,5-dioxopyrrolidin-1-yl)ethyl]cyclopentadienyl}rhodium · ligand · 2 copies · chains A, B
- BA · Barium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.63 | 0.78 | 61 | empty |
| 2 | 297 | 0.62 | 0.79 | 31 | RMD |
| 3 | 275 | 0.62 | 0.79 | 26 | RMD |
Interfaces
1 interface between chains.
- A–B · 1014 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3WJC · Crystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158L covalently linked with… · the same entry in another collection · chain A against A, TM-score 1.00
- O64527 · AlphaFold monomer V2.0 prediction for UPF0678 fatty acid-binding protein-like protein… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O64527
- Elsewhere: RCSB PDB 3WJC · PDBe 3WJC · UniProt O64527
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