1C1U: Alpha thrombin

Recruiting zinc to mediate potent, specific inhibition of serine proteases. Determined by X-ray diffraction at 1.75 Å resolution. Released 26 Jul 2000.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Homo sapiens, Hirudo medicinalis
Chains: 3
Atoms: 2,744
Mol. weight: 35.75 kDa
Ligands: BAI, ZN
Released: 26 Jul 2000

Explore 1C1U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1C1U contains 15 α-helices and 27 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 H: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	3
β-strand	20-21	2	4
β-strand	30-35	6	5
β-strand	39-46	8	5
β-strand	51-54	4	5
α-helix	56-58	3
β-strand	60-60A	2	6
α-helix	60B-60D	3
β-strand	60F-60G	2	6
α-helix	61-63	3
β-strand	64-68	5	5
β-strand	72	1	7
β-strand	81-83	3	5
β-strand	85-90	6	5
β-strand	95	1	8
β-strand	100	1	8
β-strand	104-108	5	5
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	4
β-strand	123	1	2
α-helix	124	1
α-helix	126-129C	7
β-strand	135-140	6	4
β-strand	159	1	7
β-strand	161-167	7	4
α-helix	170-174	5
β-strand	185-188	4	4
α-helix	192-192B	3
β-strand	195	1	3
β-strand	204-208	5	4
β-strand	213-221	9	4
β-strand	232-236	5	4
α-helix	238-240	3
α-helix	241-251	11

Chain I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	56-58	3
α-helix	61-63	3

Chain L: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1G	1	1
β-strand	1F	1	2
β-strand	1D	1	1
α-helix	8-10	3
α-helix	14C-14I	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha thrombin	L	protein	36	Homo sapiens	P00734 (AlphaFold model)
Alpha thrombin	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Acetyl hirudin	I	protein	11	Hirudo medicinalis	P28504 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1C1U_1 ALPHA THROMBIN (chains L)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>1C1U_2 ALPHA THROMBIN (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (I), FASTA

>1C1U_3 ACETYL HIRUDIN (chains I)
DFEEIPEEYLQ

Ligands and cofactors

ID	Name	Formula	Copies
BAI	(5-amidino-2-BENZIMIDAZOLYL)(2-benzimidazolyl)methane	C16 H14 N6	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Design of potent selective zinc-mediated serine protease inhibitors. Katz, B.A., Clark, J.M., Finer-Moore, J.S. et al. Nature (1998) 391:608-612. DOI 10.1038/35422 · 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

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