MolNFT v1 · #126929 · protein

Fxiiia in complex with the inhibitor ZED2369

5MHO · Coagulation factor xiii a chain: “Fxiiia in complex with the inhibitor ZED2369”. X-ray diffraction, 5 ligands (TRM, 1TX, CA), 10 pockets (best druggability 0.64). MolNFT v1 #126929 on GenesisL1: 3D structure, binding sites and…

PDB: 5MHO
Type: protein
Length: 1,365 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor xiii a chain; Inhibitor ZED2369
EC: 2.3.2.13
UniProt: P00488
Ligands: TRM, 1TX, CA, SO4, NH2
Pockets: 10 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor xiii a chain (EC 2.3.2.13)	protein	678	16% helix, 39% strand	P00488
B	Coagulation factor xiii a chain (EC 2.3.2.13)	protein	676	16% helix, 40% strand	P00488
G	Inhibitor ZED2369	protein	5	0% helix, 20% strand	—
H	Inhibitor ZED2369	protein	6	0% helix, 17% strand	—

Ligands and binding sites

TRM · 1H-benoximidazole-2-carboxylic acid · ligand · 2 copies · chains A, G, B, H
1TX · (2S)-2-amino-7-methoxy-7-oxoheptanoic acid · ligand · 2 copies · chains A, G, B, H
CA · Calcium ion · metal · 6 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
NH2 · Amino group · ion · chains B, H

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	408	0.64	0.78	56	empty
2	413	0.60	0.76	52	empty
3	262	0.57	0.78	30	empty
4	66	0.41	0.80	15	TRM, 1TX
5	69	0.41	0.80	23	empty

Interfaces

3 interfaces between chains.

A–B · 698 Å² buried · 7 hydrogen bonds · protein-protein
B–H · 417 Å² buried · 5 hydrogen bonds · protein-protein
A–G · 327 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5MHO · FXIIIa in complex with the inhibitor ZED2369 · 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 0.69

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 P00488
Elsewhere: RCSB PDB 5MHO · PDBe 5MHO · UniProt P00488

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