1G32: Thrombin inhibitor complex

Thrombin inhibitor complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Oct 2001.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Hirudo medicinalis
Chains: 3
Atoms: 2,702
Mol. weight: 35.79 kDa
Ligands: R11
Released: 23 Oct 2001

Explore 1G32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1G32 contains 16 α-helices and 23 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14H	6

Chain B: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-46	8	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	60-60A	2	4
α-helix	60B-60D	3
β-strand	60F-60G	2	4
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-83	3	3
β-strand	85-90	6	3
β-strand	95	1	6
β-strand	100	1	6
β-strand	104-108	5	3
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	165-169	5
β-strand	180-183	4	2
α-helix	186-186B	3
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-245	11

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	256-260	5
α-helix	261-263	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin	A	protein	36	Homo sapiens	P00734 (AlphaFold model)
Prothrombin	B	protein	259	Homo sapiens	P00734 (AlphaFold model)
Hirudin iib	C	protein	11	Hirudo medicinalis	P28504 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1G32_1 PROTHROMBIN (chains A)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B), FASTA

>1G32_2 PROTHROMBIN (chains B)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (C), FASTA

>1G32_3 HIRUDIN IIB (chains C)
DFEEIPEEYLQ

Ligands and cofactors

ID	Name	Formula	Copies
R11	4-{[1-methyl-5-(2-methyl-benzoimidazol-1-ylmethyl)-1H-benzoimidazol-2-ylmethyl]…	C25 H25 N7	1

Primary citation

Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors. Nar, H., Bauer, M., Schmid, A. et al. Structure (2001) 9:29-38. DOI 10.1016/S0969-2126(00)00551-7 · PubMed

Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AFY 1.12 Å, Thrombin in complex with 3-chloro-benzamide
4UD9 1.12 Å, Thrombin in complex with 5-chlorothiophene-2-carboxamide
4UE7 1.13 Å, Thrombin in complex with 1-amidinopiperidine
4UDW 1.16 Å, Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2,…
4UEH 1.16 Å, Thrombin in complex with benzamidine
5AF9 1.18 Å, Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide
3RM2 1.23 Å, Human Thrombin in complex with MI003
5AHG 1.24 Å, Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
2BVR 1.25 Å, Human thrombin complexed with fragment-based small molecules occupying the S1 pocket
3VXE 1.25 Å, Human alpha-thrombin-Bivalirudin complex at PD5.0
2UUF 1.26 Å, Thrombin-hirugen binary complex at 1.26A resolution
3SI4 1.27 Å, Human Thrombin In Complex With UBTHR104

Browse structure collections

About this viewer

MolViewer shows 1G32 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.