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Structural basis of na+ activation mimicry in murine thrombin

Analyse Structural basis of na+ activation mimicry in murine thrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OCV
Type: protein
Length: 284 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin
UniProt: P19221
Ligands: NAG
Pockets: 4 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombin	protein	39	36% helix, 0% strand	P19221
B	Thrombin	protein	245	14% helix, 34% strand	P19221

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.47	0.80	21	empty
2	53	0.35	0.79	16	empty
3	56	0.30	0.75	18	empty
4	61	0.29	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1535 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

2OCV · Structural basis of Na+ activation mimicry in murine thrombin · the same entry in another collection · chain A against A, TM-score 1.00
P19221 · AlphaFold monomer V2.0 prediction for prothrombin (P19221) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P19221
Elsewhere: RCSB PDB 2OCV · PDBe 2OCV · UniProt P19221

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