Research workbench
ASPARTYL/ASPARAGINYL beta-hydroxylase (asph) oxygenase and tpr domains in complex with manganese, 3-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39MER-4SER)
Analyse ASPARTYL/ASPARAGINYL beta-hydroxylase (asph) oxygenase and tpr domains in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BMI
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASPARTYL/ASPARAGINYL beta-hydroxylase; Coagulation factor X
- EC
- 1.14.11.16, 3.4.21.6
- UniProt
- Q12797, P00742
- Ligands
- U4B, MN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASPARTYL/ASPARAGINYL beta-hydroxylase (EC 1.14.11.16) | protein | 429 | 53% helix, 16% strand | Q12797 |
| B | Coagulation factor X (EC 3.4.21.6) | protein | 18 | 0% helix, 0% strand | P00742 |
Ligands and binding sites
- U4B · 3-fluoranylpyridine-2,4-dicarboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.74 | 0.99 | 18 | MN, U4B |
| 2 | 154 | 0.58 | 0.83 | 41 | empty |
| 3 | 95 | 0.42 | 0.78 | 21 | empty |
| 4 | 54 | 0.30 | 0.76 | 12 | empty |
| 5 | 83 | 0.30 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1225 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7BMI · Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12797 · AlphaFold monomer V2.0 prediction for ASPARTYL/ASPARAGINYL beta- hydroxylase (Q12797) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain B against A, TM-score 0.20
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 Q12797
- Every structure of UniProt P00742
- Elsewhere: RCSB PDB 7BMI · PDBe 7BMI · UniProt Q12797 · UniProt P00742
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