3U8O: Human thrombin

Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr. Determined by X-ray diffraction at 1.28 Å resolution. Released 23 May 2012.

Method: X-ray diffraction
Resolution: 1.28 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 2,937
Mol. weight: 34.46 kDa
Ligands: MRD, NAG
Released: 23 May 2012

Explore 3U8O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3U8O contains 14 α-helices and 26 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, 25 β-strands

Element	Residues	Length	Sheet
β-strand	322	1	1
β-strand	325-326	2	2
α-helix	327-328	2
β-strand	335-340	6	3
β-strand	345-352	8	3
β-strand	357-360	4	3
α-helix	362-364	3
β-strand	366-367	2	4
α-helix	368-370	3
β-strand	372-373	2	4
α-helix	376-378	3
β-strand	379-383	5	3
β-strand	387	1	5
β-strand	397-399	3	3
β-strand	401-406	6	3
β-strand	411	1	6
β-strand	417	1	6
β-strand	421-425	5	3
α-helix	428-431	4
β-strand	432	1	7
β-strand	435	1	7
α-helix	437-438	2
β-strand	439	1	2
α-helix	440-442	3
α-helix	443-449	7
β-strand	455-460	6	2
β-strand	479	1	5
β-strand	481-487	7	2
α-helix	490-495	6
β-strand	505-508	4	2
α-helix	512-514	3
β-strand	519	1	1
β-strand	528-532	5	2
β-strand	539-547	9	2
β-strand	558-562	5	2
α-helix	564-566	3
α-helix	567-577	11

Chain I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	300-302	3
α-helix	309-318	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	L	protein	30	Homo sapiens	P00734 (AlphaFold model)
Thrombin heavy chain	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
D-phe-pro-D-arg-D-thr derived direct thrombin inhibitor	I	protein	5	synthetic construct

Sequence of entity 1 (L), FASTA

>3U8O_1 Thrombin light chain (chains L)
ADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>3U8O_2 Thrombin heavy chain (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (I), FASTA

>3U8O_3 D-PHE-PRO-D-ARG-D-THR DERIVED DIRECT THROMBIN INHIBITOR (chains I)
FPRTX

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors. Figueiredo, A.C., Clement, C.C., Zakia, S. et al. PLoS One (2012) 7:e34354-e34354. DOI 10.1371/journal.pone.0034354 · 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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