Research workbench

Staphylocoagulase-prethrombin-2 complex

Analyse Staphylocoagulase-prethrombin-2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NU9
Type: protein
Length: 1,142 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light and heavy chains; Staphylocoagulase
EC: 3.4.21.5
UniProt: P00734, Q846V4
Ligands: 0ZJ, HG
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Thrombin light and heavy chains (EC 3.4.21.5)	protein	290	17% helix, 30% strand	P00734
C, F	Staphylocoagulase	protein	281	67% helix, 1% strand	Q846V4

Ligands and binding sites

0ZJ · N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains A, C, D, F
HG · Mercury (II) ion · metal · 4 copies · chains C, A, F, D
IMD · Imidazole · additive · 6 copies · chains C, F

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	526	0.70	0.79	55	empty
2	73	0.66	0.93	21	empty
3	516	0.66	0.77	68	IMD
4	455	0.65	0.78	55	0ZJ, HG
5	441	0.65	0.78	47	0ZJ, HG

Interfaces

3 interfaces between chains.

D–F · 2202 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 2195 Å² buried · 33 hydrogen bonds · protein-protein
C–F · 675 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1NU9 · Staphylocoagulase-Prethrombin-2 complex · the same entry in another collection · chain A against A, TM-score 1.00
P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain D against A, TM-score 0.91

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 Q846V4
Elsewhere: RCSB PDB 1NU9 · PDBe 1NU9 · UniProt P00734 · UniProt Q846V4

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