MolNFT v1 · #14668 · protein

Crystal structure of the anticoagulant slow form of thrombin

1MH0 · Prothrombin: “Crystal structure of the anticoagulant slow form of thrombin”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.56). MolNFT v1 #14668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1MH0
Type: protein
Length: 554 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prothrombin
EC: 3.4.21.5
UniProt: P00734
Ligands: NAG
Pockets: 5 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Prothrombin (EC 3.4.21.5)	protein	277	13% helix, 32% strand	P00734

Ligands and binding sites

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

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

Pockets

5 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	265	0.56	0.77	41	empty
2	271	0.56	0.77	38	empty
3	99	0.37	0.75	25	empty
4	116	0.36	0.73	22	empty
5	54	0.29	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 649 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1MH0 · Crystal structure of the anticoagulant slow form of thrombin · the same entry in another collection · chain A against A, TM-score 1.00

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
Elsewhere: RCSB PDB 1MH0 · PDBe 1MH0 · UniProt P00734

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