MolNFT v1 · #117980 · protein

Human plasma coagulation fxi with peptide LP2

5EOD · Coagulation factor XI: “Human plasma coagulation fxi with peptide LP2”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.81). MolNFT v1 #117980 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EOD
Type: protein
Length: 592 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor XI; LP2
EC: 3.4.21.27
UniProt: P03951
Ligands: NAG
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor XI (EC 3.4.21.27)	protein	586	16% helix, 37% strand	P03951
B	LP2	protein	6	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	691	0.81	0.86	62	empty
2	472	0.71	0.81	42	empty
3	368	0.64	0.79	49	empty
4	176	0.57	0.81	30	empty
5	99	0.39	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 468 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5EOD · Human Plasma Coagulation FXI with peptide LP2 · 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 A against A, TM-score 0.69

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 5EOD · PDBe 5EOD · UniProt P03951

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