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Human factor xiii with calcium bound in the ion site

Analyse Human factor xiii with calcium bound in the ion site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EVU
Type: protein
Length: 1,416 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor xiii
EC: 2.3.2.13
UniProt: P00488
Ligands: CA
Pockets: 17 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor xiii (EC 2.3.2.13)	protein	708	15% helix, 41% strand	P00488
B	Coagulation factor xiii (EC 2.3.2.13)	protein	708	15% helix, 42% strand	P00488

Ligands and binding sites

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

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	977	0.86	0.87	124	PGO
2	822	0.85	0.88	104	empty
3	453	0.68	0.80	39	empty
4	130	0.65	0.88	28	empty
5	128	0.61	0.86	35	empty

Interfaces

1 interface between chains.

A–B · 2894 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (acetylation).

Compared structures

1EVU · Human factor xiii with calcium bound in the ion site · 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 B 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 1EVU · PDBe 1EVU · UniProt P00488

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