MolNFT v1 · #161277 · protein
ASPARTYL/ASPARAGINYL beta-hydroxylase (asph) H679A in complex with mn, nog and factor X peptide fragment (39MER-4SER)
6Q9F: “ASPARTYL/ASPARAGINYL beta-hydroxylase (asph) H679A in complex with mn, nog and factor X peptide fragment…”. X-ray diffraction, 2 ligands (OGA, MN), 5 pockets (best druggability 0.74). MolNFT v1 #161277 on GenesisL1: 3D structure…
- PDB
- 6Q9F
- Type
- protein
- Length
- 449 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
- OGA, MN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% 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 | 20 | 0% helix, 0% strand | P00742 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A, B
- GOL · Glycerol · additive · 3 copies · 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 | 69 | 0.74 | 0.98 | 21 | MN, OGA |
| 2 | 120 | 0.59 | 0.86 | 31 | GOL |
| 3 | 96 | 0.42 | 0.78 | 23 | empty |
| 4 | 94 | 0.36 | 0.75 | 23 | empty |
| 5 | 79 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1351 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6Q9F · Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X… · the same entry in another collection · chain B against B, 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 0.19
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 6Q9F · PDBe 6Q9F · UniProt Q12797 · UniProt P00742
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