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Structure of human plasma factor xiia in complex with (2S)-4-(5- chloro-1,3-benzoxazol-2-yl)-1-(N,3-dicyclohexyl-D-alanyl)-N- [(thiophen-2-YL)METHYL]PIPERAZINE-2-carboxamide (compound 7)

Analyse Structure of human plasma factor xiia in complex with (2S)-4-(5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X0S
Type: protein
Length: 718 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor XII
EC: 3.4.21.38
UniProt: P00748
Ligands: UJA, SO4
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor XII (EC 3.4.21.38)	protein	241	11% helix, 34% strand	P00748
B	Coagulation factor XII (EC 3.4.21.38)	protein	237	11% helix, 34% strand	P00748
C	Coagulation factor XII (EC 3.4.21.38)	protein	240	11% helix, 35% strand	P00748

Ligands and binding sites

UJA · (2S)-4-(5-chloro-1,3-benzoxazol-2-yl)-1-(N,3-dicyclohexyl-D-alanyl)-N-[(thiophen-2-yl) methyl]piperazine-2-carboxamide · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1053	0.75	0.78	88	empty
2	103	0.42	0.78	22	UJA
3	119	0.42	0.76	31	UJA
4	79	0.38	0.77	19	UJA

Interfaces

3 interfaces between chains.

B–C · 273 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 254 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 253 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide (disulfide).

Compared structures

6X0S · Structure of human plasma factor XIIa in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P00748 · AlphaFold monomer V2.0 prediction for coagulation factor XII (P00748) · a predicted model of the same protein · chain B 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 P00748
Elsewhere: RCSB PDB 6X0S · PDBe 6X0S · UniProt P00748

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