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Fxia antibody complex

Analyse Fxia antibody complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AOD
Type: protein
Length: 654 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fxia antibody Fab light chain; Fxia antibody Fab heavy chain; Coagulation factor XI
EC: 3.4.21.27
UniProt: P03951
Ligands: CO, PO4, SO4
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fxia antibody Fab light chain	protein	207	8% helix, 52% strand	—
B	Fxia antibody Fab heavy chain	protein	211	11% helix, 51% strand	—
C	Coagulation factor XI (EC 3.4.21.27)	protein	236	13% helix, 35% strand	P03951

Ligands and binding sites

CO · Cobalt (II) ion · metal · 3 copies · chains B, C
PO4 · Phosphate ion · ion · 5 copies · chains B, C
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
GOL · Glycerol · additive · 9 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	583	0.63	0.75	69	empty
2	252	0.61	0.80	33	GOL
3	87	0.54	0.85	27	empty
4	200	0.49	0.76	32	SO4, GOL
5	192	0.46	0.74	28	GOL

Interfaces

3 interfaces between chains.

A–B · 1747 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1045 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 376 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6AOD · FXIa antibody complex · the same entry in another collection · chain A against A, TM-score 1.00
P03951 · AlphaFold monomer V2.0 prediction for coagulation factor XI (P03951) · a predicted model of the same protein · chain C 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 P03951
Elsewhere: RCSB PDB 6AOD · PDBe 6AOD · UniProt P03951

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