3LU9: Human thrombin mutant S195A
Crystal structure of human thrombin mutant S195A in complex with the extracellular fragment of human PAR1. Determined by X-ray diffraction at 1.8 Å resolution. Released 16 Mar 2010.
- Method
- X-ray diffraction
- Resolution
- 1.8 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 5,949
- Mol. weight
- 76.84 kDa
- Ligands
- NAG
- Released
- 16 Mar 2010
Explore 3LU9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3LU9 contains 35 α-helices and 48 β-strands across 6 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 | 8-10 | 3 | |
| α-helix | 12-14 | 3 | |
| α-helix | 14C-14K | 9 | |
Chain B: 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 | 65-68 | 4 | 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 | 123-125 | 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 |
| α-helix | 184A-185 | 2 | |
| β-strand | 189 | 1 | 1 |
| β-strand | 198-202 | 5 | 2 |
| β-strand | 207-216 | 10 | 2 |
| β-strand | 226-230 | 5 | 2 |
| α-helix | 232-234 | 3 | |
| α-helix | 235-244 | 10 | |
Chain C: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 39-40 | 2 | 2 |
| α-helix | 52-54 | 3 | |
Chain D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1J-1G | 4 | |
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14K | 9 | |
Chain E: 12 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17 | 1 | 8 |
| β-strand | 20-21 | 2 | 9 |
| α-helix | 22-23 | 2 | |
| β-strand | 30-35 | 6 | 10 |
| β-strand | 39-46 | 8 | 10 |
| β-strand | 51-54 | 4 | 10 |
| α-helix | 56-58 | 3 | |
| β-strand | 60-60A | 2 | 11 |
| α-helix | 60B-60D | 3 | |
| β-strand | 60F-60G | 2 | 11 |
| α-helix | 61-63 | 3 | |
| β-strand | 64-68 | 5 | 10 |
| β-strand | 72 | 1 | 12 |
| β-strand | 81-90 | 10 | 10 |
| β-strand | 95 | 1 | 13 |
| β-strand | 100 | 1 | 13 |
| β-strand | 104-108 | 5 | 10 |
| α-helix | 111-114 | 4 | |
| α-helix | 120-121 | 2 | |
| β-strand | 122 | 1 | 9 |
| α-helix | 123-124 | 2 | |
| α-helix | 126-129C | 7 | |
| β-strand | 135-140 | 6 | 9 |
| β-strand | 154 | 1 | 12 |
| β-strand | 156-162 | 7 | 9 |
| α-helix | 165-170 | 6 | |
| α-helix | 175-176 | 2 | |
| β-strand | 180-183 | 4 | 9 |
| β-strand | 189 | 1 | 8 |
| β-strand | 198-202 | 5 | 9 |
| β-strand | 207-216 | 10 | 9 |
| β-strand | 226-230 | 5 | 9 |
| α-helix | 232-234 | 3 | |
| α-helix | 235-245 | 11 | |
Chain F: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-37 | 3 | |
| β-strand | 39-40 | 2 | 9 |
| α-helix | 52-54 | 3 | |
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 | 25 | Homo sapiens | P25116 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>3LU9_1 Prothrombin (chains A, D)
SEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Sequence of entity 2 (B, E), FASTA
>3LU9_2 Prothrombin (chains B, E)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
Sequence of entity 3 (C, F), FASTA
>3LU9_3 Proteinase-activated receptor 1 (chains C, F)
ATNATLDPRSFLLRNPNDKYEPFWE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
Water and common crystallization additives (NA, GOL) are not listed.
Primary citation
Crystal structure of thrombin bound to the uncleaved extracellular fragment of PAR1. Gandhi, P.S., Chen, Z., Di Cera, E. J Biol Chem (2010) 285:15393-15398. DOI 10.1074/jbc.M110.115337 · 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
Browse structure collections
About this viewer
MolViewer shows 3LU9 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.