MolNFT v1 · #47600 · protein

Crystal structure of the factor XA/NAP5 complex

2P3F · Coagulation factor X: “Crystal structure of the factor XA/NAP5 complex”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.51). MolNFT v1 #47600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2P3F
Type: protein
Length: 360 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor X; Anti-coagulant protein 5
EC: 3.4.21.6
UniProt: P00742, Q16940
Ligands: NA
Pockets: 6 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Coagulation factor X (EC 3.4.21.6)	protein	235	12% helix, 36% strand	P00742
L	Coagulation factor X (EC 3.4.21.6)	protein	51	0% helix, 27% strand	P00742
N	Anti-coagulant protein 5	protein	74	14% helix, 22% strand	Q16940

Ligands and binding sites

NA · Sodium ion · metal · chains H

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

Pockets

6 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	178	0.51	0.78	29	empty
2	145	0.50	0.79	23	empty
3	77	0.42	0.79	15	empty
4	94	0.39	0.76	22	empty
5	66	0.39	0.79	16	empty

Interfaces

2 interfaces between chains.

H–N · 970 Å² buried · 25 hydrogen bonds · protein-protein
H–L · 875 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide (disulfide).

Compared structures

2P3F · Crystal structure of the factor Xa/NAP5 complex · the same entry in another collection · chain H against H, 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

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 Q16940
Elsewhere: RCSB PDB 2P3F · PDBe 2P3F · UniProt P00742 · UniProt Q16940

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