3BEF: Thrombin
Crystal structure of thrombin bound to the extracellular fragment of PAR1. Determined by X-ray diffraction at 2.2 Å resolution. Released 1 Jan 2008.
- Method
- X-ray diffraction
- Resolution
- 2.2 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 5,186
- Mol. weight
- 73.19 kDa
- Ligands
- NAG
- Released
- 1 Jan 2008
Explore 3BEF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3BEF contains 30 α-helices and 46 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: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1J-1G | 4 | |
| α-helix | 1C-1A | 3 | |
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14H | 6 | |
Chain B: 11 helices, 23 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 | 56-59 | 4 | |
| β-strand | 60-60A | 2 | 4 |
| α-helix | 60B-60D | 3 | |
| β-strand | 60F-60G | 2 | 4 |
| 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 | 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 | 123-125 | 3 | |
| 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 |
| 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 | 235-242 | 8 | |
Chain C: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 52-54 | 3 | |
Chain D: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1J-1G | 4 | |
| α-helix | 1C-1A | 3 | |
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14K | 9 | |
Chain E: 10 helices, 23 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 | 56-58 | 3 | |
| β-strand | 60 | 1 | 10 |
| β-strand | 60G | 1 | 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 | 95 | 1 | 12 |
| β-strand | 100 | 1 | 12 |
| β-strand | 104-108 | 5 | 9 |
| α-helix | 111-114 | 4 | |
| α-helix | 120-121 | 2 | |
| β-strand | 122 | 1 | 8 |
| α-helix | 123-124 | 2 | |
| α-helix | 126-129C | 7 | |
| β-strand | 135-140 | 6 | 8 |
| β-strand | 154 | 1 | 11 |
| β-strand | 156-162 | 7 | 8 |
| α-helix | 165-171 | 7 | |
| β-strand | 180-183 | 4 | 8 |
| β-strand | 189 | 1 | 7 |
| β-strand | 198-202 | 5 | 8 |
| β-strand | 207-213 | 7 | 8 |
| β-strand | 226-230 | 5 | 8 |
| α-helix | 231-234 | 4 | |
| α-helix | 235-242 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Prothrombin | A, D | protein | 46 | Homo sapiens | P00734 (AlphaFold model) |
| Prothrombin | B, E | protein | 259 | Homo sapiens | P00734 (AlphaFold model) |
| Proteinase-activated receptor 1 | C, F | protein | 9 | Homo sapiens | P25116 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>3BEF_1 Prothrombin (chains A, D)
SEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Sequence of entity 2 (B, E), FASTA
>3BEF_2 Prothrombin (chains B, E)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRNIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
Sequence of entity 3 (C, F), FASTA
>3BEF_3 Proteinase-activated receptor 1 (chains C, F)
NDKYEPFWE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
Primary citation
Structural identification of the pathway of long-range communication in an allosteric enzyme. Gandhi, P.S., Chen, Z., Mathews, F.S. et al. Proc Natl Acad Sci U S A (2008) 105:1832-1837. DOI 10.1073/pnas.0710894105 · 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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