MolNFT v1 · #7316 · protein

Thrombin inhibitor complex

1G30 · Prothrombin: “Thrombin inhibitor complex”. X-ray diffraction, 1 ligand (T87), 2 pockets (best druggability 0.54). MolNFT v1 #7316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1G30
Type: protein
Length: 289 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prothrombin; Hirudin iib
EC: 3.4.21.5
UniProt: P00734, P28506
Ligands: T87
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prothrombin (EC 3.4.21.5)	protein	27	33% helix, 0% strand	P00734
B	Prothrombin (EC 3.4.21.5)	protein	252	14% helix, 35% strand	P00734
C	Hirudin iib	protein	10	30% helix, 0% strand	P28506

Ligands and binding sites

T87 · [(1-{2[(4-carbamimidoyl-phenylamino)-methyl]-1-methyl-1H-benzoimidazol-5-yl}-cyclopropyl)-pyridin-2-yl-methyleneaminooxy]-acetic acid ethyl ester · ligand · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	230	0.54	0.77	37	T87
2	59	0.30	0.75	14	empty

Interfaces

2 interfaces between chains.

A–B · 1124 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 641 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).

Compared structures

1G30 · Thrombin inhibitor complex · the same entry in another collection · chain A against A, TM-score 1.00
P28506 · AlphaFold monomer V2.0 prediction for hirudin-2B (P28506) · a predicted model of the same protein · chain C against A, TM-score 0.55

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 P28506
Elsewhere: RCSB PDB 1G30 · PDBe 1G30 · UniProt P00734 · UniProt P28506

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