MolNFT v1 · #161458 · protein
Crystal structures of the recombinant beta-factor xiia protease with bound thr-arg and pro-arg substrate mimetics
6QF7 · Maltodextrin-binding protein: “Crystal structures of the recombinant beta-factor xiia protease with bound thr-arg and pro-arg substrate…”. X-ray diffraction, 3 ligands (0G6, GLC, NAG), 17 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6QF7
- Type
- protein
- Length
- 1,227 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding protein; Coagulation factor XII
- EC
- 3.4.21.38
- UniProt
- A0A376KDN7, P00748
- Ligands
- 0G6, GLC, NAG
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltodextrin-binding protein | protein | 369 | 43% helix, 18% strand | A0A376KDN7 |
| B, D | Coagulation factor XII (EC 3.4.21.38) | protein | 244 | 7% helix, 34% strand | P00748 |
| C | Maltodextrin-binding protein | protein | 370 | 41% helix, 16% strand | A0A376KDN7 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains B, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.78 | 0.87 | 49 | GLC |
| 2 | 530 | 0.75 | 0.83 | 54 | GLC |
| 3 | 168 | 0.58 | 0.81 | 29 | empty |
| 4 | 287 | 0.55 | 0.76 | 28 | empty |
| 5 | 335 | 0.55 | 0.75 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 945 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 910 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 186 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 181 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6QF7 · Crystal structures of the recombinant beta-Factor XIIa protease with bound Thr-Arg and… · the same entry in another collection · chain B against B, TM-score 1.00
- P00748 · AlphaFold monomer V2.0 prediction for coagulation factor XII (P00748) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 A0A376KDN7
- Every structure of UniProt P00748
- Elsewhere: RCSB PDB 6QF7 · PDBe 6QF7 · UniProt A0A376KDN7 · UniProt P00748
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