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Staphylocoagulase-thrombin complex

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

PDB: 1NU7
Type: protein
Length: 1,135 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain; Staphylocoagulase
EC: 3.4.21.5
UniProt: P00734, Q846V4
Ligands: 0ZJ, HG
Pockets: 17 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombin light chain (EC 3.4.21.5)	protein	28	36% helix, 0% strand	P00734
B, F	Thrombin heavy chain (EC 3.4.21.5)	protein	258	16% helix, 34% strand	P00734
D, H	Staphylocoagulase	protein	282	67% helix, 1% strand	Q846V4
E	Thrombin light chain (EC 3.4.21.5)	protein	27	33% helix, 0% strand	P00734

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 B, D, F, H
HG · Mercury (II) ion · metal · 4 copies · chains B, D, F, H
IMD · Imidazole · additive · 6 copies · chains D, H

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	689	0.71	0.78	80	empty
2	544	0.70	0.80	50	empty
3	488	0.67	0.78	58	0ZJ, HG
4	518	0.66	0.77	64	IMD
5	457	0.65	0.78	53	0ZJ, HG

Interfaces

5 interfaces between chains.

B–D · 1805 Å² buried · 23 hydrogen bonds · protein-protein
F–H · 1783 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1165 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1165 Å² buried · 24 hydrogen bonds · protein-protein
D–H · 673 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1NU7 · Staphylocoagulase-Thrombin Complex · the same entry in another collection · chain H against H, TM-score 1.00
P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain F 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 1NU7 · PDBe 1NU7 · UniProt P00734 · UniProt Q846V4

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