3VXE: Thrombin light chain

Human alpha-thrombin-Bivalirudin complex at PD5.0. Determined by X-ray diffraction at 1.25 Å resolution. Released 4 Sept 2013.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,722
Mol. weight: 36.3 kDa
Ligands: NAG
Released: 4 Sept 2013

Explore 3VXE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VXE contains 16 α-helices and 25 β-strands across 4 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: 13 helices, 24 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
β-strand	115	1	7
β-strand	118	1	7
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	156-163	8	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	235-244	10

Chain I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2

Chain J: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	56-60	5

Chain L: 2 helices, 0 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	L	protein	36	Homo sapiens	P00734 (AlphaFold model)
Thrombin heavy chain	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Bivalirudin	J	protein	17		P28504 (AlphaFold model)
Bivalirudin	I	protein	3

Sequence of entity 1 (L), FASTA

>3VXE_1 Thrombin light chain (chains L)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>3VXE_2 Thrombin heavy chain (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (J), FASTA

>3VXE_3 BIVALIRUDIN (chains J)
PGGGGNGDFEEIPEEYL

Sequence of entity 4 (I), FASTA

>3VXE_4 BIVALIRUDIN (chains I)
FPR

Ligands and cofactors

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

Primary citation

Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex. Yamada, T., Kurihara, K., Ohnishi, Y. et al. Biochim Biophys Acta (2013) 1834:1532-1538. DOI 10.1016/j.bbapap.2013.05.014 · 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
2UUF 1.26 Å, Thrombin-hirugen binary complex at 1.26A resolution
3SI4 1.27 Å, Human Thrombin In Complex With UBTHR104
5JZY 1.27 Å, Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenz…

Browse structure collections

About this viewer

MolViewer shows 3VXE 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.