Research workbench
Crystal structure of molybdopterin converting factor subunit 2 (AQ_2181) from aquifex aeolicus VF5
Analyse Crystal structure of molybdopterin converting factor subunit 2 (AQ_2181) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OMD
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdopterin-converting factor subunit 2
- UniProt
- O67928
- Ligands
- NA, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Molybdopterin-converting factor subunit 2 | protein | 135 | 35% helix, 33% strand | O67928 |
| B | Molybdopterin-converting factor subunit 2 | protein | 145 | 34% helix, 29% strand | O67928 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- FMT · Formic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.61 | 0.81 | 26 | FMT, GOL |
| 2 | 225 | 0.58 | 0.80 | 25 | TRS, FMT |
| 3 | 66 | 0.37 | 0.78 | 16 | NA |
| 4 | 58 | 0.32 | 0.77 | 16 | NA |
Interfaces
1 interface between chains.
- A–B · 1490 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2OMD · Crystal structure of molybdopterin converting factor subunit 2 (aq_2181) from aquifex… · the same entry in another collection · chain A against A, TM-score 1.00
- O67928 · AlphaFold monomer V2.0 prediction for molybdopterin synthase catalytic subunit (O67928) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O67928
- Elsewhere: RCSB PDB 2OMD · PDBe 2OMD · UniProt O67928
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