1TB6: Thrombin

2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 Aug 2004.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,324
Mol. weight: 92.16 kDa
Ligands: NAG
Released: 17 Aug 2004

Explore 1TB6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TB6 contains 33 α-helices and 39 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: 12 helices, 21 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	104-108	5	3
α-helix	111-114	4
β-strand	122	1	2
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	163-164	2
α-helix	165-171	7
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 I: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	39-41	3
α-helix	46-67	22
β-strand	76-78	3	6
α-helix	80-91	12
α-helix	96-105	10
α-helix	113-117	5
α-helix	119-134	16
β-strand	139-149	11	7
β-strand	154	1	8
α-helix	156-165	10
β-strand	171-173	3	7
α-helix	179-193	15
α-helix	203	1
β-strand	213-222	10	7
α-helix	223-224	2
β-strand	225	1	9
α-helix	228-230	3
α-helix	231-233	3
β-strand	235-238	4	6
β-strand	248-262	15	6
α-helix	264-266	3
β-strand	268-273	6	6
β-strand	274	1	9
β-strand	279-285	7	6
α-helix	292-298	7
α-helix	301-310	10
β-strand	312-321	10	6
β-strand	323-330	8	7
α-helix	332-337	6
α-helix	342-344	3
β-strand	355	1	8
β-strand	366-375	10	7
β-strand	400-403	4	6
β-strand	408-414	7	6
β-strand	419-426	8	6

Chain L: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	8-10	3
α-helix	14D-14I	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
thrombin	L	protein	49	Homo sapiens	P00734 (AlphaFold model)
thrombin	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Antithrombin-III	I	protein	432	Homo sapiens	P01008 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1TB6_1 thrombin (chains L)
TATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>1TB6_2 thrombin (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (I), FASTA

>1TB6_3 Antithrombin-III (chains I)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLCVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVCFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin. Li, W., Johnson, D.J., Esmon, C.T. et al. Nat Struct Mol Biol (2004) 11:857-862. DOI 10.1038/nsmb811 · 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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