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Crystal structure of the antithrombin-S195A factor xa-pentasaccharide complex

Analyse Crystal structure of the antithrombin-S195A factor xa-pentasaccharide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GD4
Type: protein
Length: 1,414 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor X, stuart factor, stuart-prower factor, contains: factor X light…
EC: 3.4.21.6
UniProt: P00742, P01008
Ligands: ZDO, SUS, NAG, MAN, IDS, BDP, SGN, BMA, CA
Pockets: 12 · best druggability 0.66

Structure

x-ray diffraction · 6 distinct chains · 21% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Coagulation factor X, stuart factor, stuart-prower factor, contains: factor X light chain (EC 3.4.21.6)	protein	54	7% helix, 19% strand	P00742
H	Coagulation factor, stuart factor, stuart-prower factor, contains: factor X light chain (EC 3.4.21.6)	protein	234	10% helix, 32% strand	P00742
I	Antithrombin-III	protein	417	29% helix, 25% strand	P01008
A	Coagulation factor X, stuart factor, stuart-prower factor, contains: factor X light chain (EC 3.4.21.6)	protein	52	8% helix, 19% strand	P00742
B	Coagulation factor, stuart factor, stuart-prower factor, contains: factor X light chain (EC 3.4.21.6)	protein	239	10% helix, 32% strand	P00742
C	Antithrombin-III	protein	418	29% helix, 25% strand	P01008

Ligands and binding sites

ZDO · methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside · ligand · 2 copies · chains I, C
SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · 2 copies · chains I, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains I, C
MAN · alpha-D-mannopyranose · sugar · 3 copies
IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 2 copies · chains I, C
BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains I, C
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains I, C
BMA · beta-D-mannopyranose · sugar · chains I
CA · Calcium ion · metal · 2 copies · chains H, B

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	255	0.66	0.83	31	empty
2	271	0.64	0.81	31	empty
3	313	0.57	0.77	35	empty
4	296	0.56	0.76	39	empty
5	160	0.51	0.78	27	empty

Interfaces

5 interfaces between chains.

B–C · 1214 Å² buried · 34 hydrogen bonds · protein-protein
H–I · 1211 Å² buried · 34 hydrogen bonds · protein-protein
L–H · 878 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 877 Å² buried · 9 hydrogen bonds · protein-protein
I–C · 134 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 22 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

2GD4 · Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex · the same entry in another collection · chain C against C, TM-score 1.00
P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain H against A, TM-score 0.98
P01008 · AlphaFold monomer V2.0 prediction for antithrombin-III (P01008) · 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 P00742
Every structure of UniProt P01008
Elsewhere: RCSB PDB 2GD4 · PDBe 2GD4 · UniProt P00742 · UniProt P01008

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