MolNFT v1 · #11764 · protein
Structure of the covalent acyl-adenylate form of the moeb-moad protein complex
1JWB · Molybdopterin biosynthesis moeb protein: “Structure of the covalent acyl-adenylate form of the moeb-moad protein complex”. X-ray diffraction, 3 ligands (AMP, ZN, SO4), 3 pockets (best druggability 0.56). MolNFT v1 #11764 on…
- PDB
- 1JWB
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdopterin biosynthesis moeb protein; Molybdopterin [mpt] converting factor, subunit 1
- UniProt
- P12282, P30748
- Ligands
- AMP, ZN, SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Molybdopterin biosynthesis moeb protein | protein | 240 | 42% helix, 22% strand | P12282 |
| D | Molybdopterin [mpt] converting factor, subunit 1 | protein | 80 | 26% helix, 25% strand | P30748 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains B, D
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.56 | 0.81 | 31 | AMP |
| 2 | 139 | 0.44 | 0.76 | 24 | empty |
| 3 | 57 | 0.33 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- B–D · 1082 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1JWB · Structure of the Covalent Acyl-Adenylate Form of the MoeB-MoaD Protein Complex · the same entry in another collection · chain B against B, TM-score 1.00
- P12282 · AlphaFold monomer V2.0 prediction for molybdopterin-synthase adenylyltransferase (P12282) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P30748 · AlphaFold monomer V2.0 prediction for molybdopterin synthase sulfur carrier subunit… · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P12282
- Every structure of UniProt P30748
- Elsewhere: RCSB PDB 1JWB · PDBe 1JWB · UniProt P12282 · UniProt P30748
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