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The structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin complexed with thrombin

Analyse The structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HLT
Type: protein
Length: 573 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Thrombomodulin
UniProt: P00734, P07204
Ligands: 0G6
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, J	Alpha-thrombin (small subunit)	protein	27	44% helix, 0% strand	P00734
H, K	Alpha-thrombin (large subunit)	protein	251	11% helix, 33% strand	P00734
R	Thrombomodulin	protein	17	0% helix, 24% strand	P07204

Ligands and binding sites

0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains H, K

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.56	0.78	40	0G6
2	183	0.52	0.78	32	0G6
3	82	0.40	0.78	15	empty
4	75	0.38	0.77	21	empty
5	63	0.37	0.78	17	empty

Interfaces

5 interfaces between chains.

J–K · 1102 Å² buried · 22 hydrogen bonds · protein-protein
L–H · 1091 Å² buried · 19 hydrogen bonds · protein-protein
H–R · 463 Å² buried · 5 hydrogen bonds · protein-protein
K–R · 463 Å² buried · 6 hydrogen bonds · protein-protein
H–K · 135 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

1HLT · The structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin complexed… · the same entry in another collection · chain R against R, TM-score 1.00
P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain K against A, TM-score 0.92
P07204 · AlphaFold monomer V2.0 prediction for thrombomodulin (P07204) · a predicted model of the same protein · chain R against A, TM-score 0.38

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 P00734
Every structure of UniProt P07204
Elsewhere: RCSB PDB 1HLT · PDBe 1HLT · UniProt P00734 · UniProt P07204

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