2B5T: Thrombin

2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules. Determined by X-ray diffraction at 2.1 Å resolution. Released 19 Sept 2006.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,026
Mol. weight: 128.61 kDa
Ligands: NAG
Released: 19 Sept 2006

Explore 2B5T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2B5T contains 46 α-helices and 60 β-strands across 5 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	8-10	3
α-helix	14C-14H	6

Chain B: 13 helices, 22 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	81-90	10	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	123-124	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	165-170	6
α-helix	175-176	2
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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	8-10	3
α-helix	14D-14H	5

Chain D: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	7
β-strand	20-21	2	8
α-helix	22-23	2
β-strand	30-35	6	9
β-strand	39-46	8	9
β-strand	51-54	4	9
α-helix	56-59	4
β-strand	60-60A	2	10
α-helix	60B-60D	3
β-strand	60F-60G	2	10
α-helix	61-63	3
β-strand	64-68	5	9
β-strand	72	1	11
β-strand	81-83	3	9
β-strand	85-90	6	9
β-strand	104-108	5	9
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	8
α-helix	126-129C	7
β-strand	135-140	6	8
β-strand	154	1	11
β-strand	156-162	7	8
α-helix	165-170	6
β-strand	180-183	4	8
β-strand	189	1	7
β-strand	198-202	5	8
β-strand	207-215	9	8
β-strand	226-230	5	8
α-helix	232-234	3
α-helix	235-245	11

Chain I: 17 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	40-41	2
α-helix	46-68	23
β-strand	76-78	3	12
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
α-helix	113-117	5
α-helix	119-130	12
β-strand	138-149	12	13
α-helix	156-166	11
α-helix	169-170	2
β-strand	171-173	3	13
α-helix	179-193	15
β-strand	213-224	12	13
β-strand	225	1	14
α-helix	228-230	3
α-helix	231-233	3
β-strand	235-239	5	12
β-strand	247-262	16	12
α-helix	264-266	3
β-strand	268-273	6	12
β-strand	274	1	14
β-strand	279-285	7	12
α-helix	292-298	7
α-helix	301-310	10
β-strand	312-321	10	12
β-strand	323-326	4	13
α-helix	331-336	6
α-helix	342-344	3
β-strand	366-375	10	13
β-strand	379-380	2	13
β-strand	402-403	2	12
β-strand	408-414	7	12
β-strand	420-426	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin	A, C	protein	49	Homo sapiens	P00734 (AlphaFold model)
Thrombin	B, D	protein	259	Homo sapiens	P00734 (AlphaFold model)
Antithrombin-III	I	protein	432	Homo sapiens	P01008 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2B5T_1 Thrombin (chains A, C)
TATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B, D), FASTA

>2B5T_2 Thrombin (chains B, D)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (I), FASTA

>2B5T_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 (SO4, GOL) are not listed.

Primary citation

Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation. Johnson, D.J., Langdown, J., Li, W. et al. J Biol Chem (2006) 281:35478-35486. DOI 10.1074/jbc.M607204200 · 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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