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Human factor xiii, mutant W279F zymogen

Analyse Human factor xiii, mutant W279F zymogen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EX0
Type: protein
Length: 1,421 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor xiii a chain
EC: 2.3.2.13
UniProt: P00488
Ligands: CA, PO4
Pockets: 19 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor xiii a chain (EC 2.3.2.13)	protein	705	15% helix, 42% strand	P00488
B	Coagulation factor xiii a chain (EC 2.3.2.13)	protein	716	15% helix, 42% strand	P00488

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 3 copies · chains A, B
PGO · S-1,2-propanediol · additive · 6 copies · chains A, B

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1152	0.87	0.88	142	empty
2	959	0.77	0.80	75	PGO
3	252	0.68	0.84	28	empty
4	420	0.64	0.78	34	empty
5	148	0.64	0.86	30	empty

Interfaces

1 interface between chains.

A–B · 2584 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

1EX0 · Human factor xiii, mutant W279F zymogen · the same entry in another collection · chain A against A, TM-score 1.00
P00488 · AlphaFold monomer V2.0 prediction for coagulation factor xiii a chain (P00488) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00488
Elsewhere: RCSB PDB 1EX0 · PDBe 1EX0 · UniProt P00488

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