1HLT: Alpha-thrombin
The structure of a nonadecapeptide of the fifth egf domain of thrombomodulin complexed with thrombin. Determined by X-ray diffraction at 3.0 Å resolution. Released 20 Dec 1994.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 4,756
- Mol. weight
- 68.99 kDa
- Ligands
- 0G6
- Released
- 20 Dec 1994
Explore 1HLT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1HLT contains 22 α-helices and 44 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 H: 8 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 | 30-36 | 7 | 3 |
| β-strand | 38-45 | 8 | 3 |
| β-strand | 46 | 1 | 4 |
| β-strand | 51-54 | 4 | 4 |
| α-helix | 56-58 | 3 | |
| β-strand | 60A | 1 | 5 |
| β-strand | 60F | 1 | 5 |
| β-strand | 64-68 | 5 | 3 |
| β-strand | 72 | 1 | 6 |
| β-strand | 81-84 | 4 | 3 |
| β-strand | 85-90 | 6 | 4 |
| β-strand | 104-108 | 5 | 4 |
| β-strand | 122 | 1 | 2 |
| α-helix | 123-124 | 2 | |
| α-helix | 126-129C | 7 | |
| β-strand | 135-139 | 5 | 2 |
| β-strand | 154 | 1 | 6 |
| β-strand | 156-162 | 7 | 2 |
| α-helix | 163-164 | 2 | |
| α-helix | 165-171 | 7 | |
| 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 J: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| α-helix | 14C-14G | 5 | |
Chain K: 10 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17 | 1 | 7 |
| β-strand | 20-21 | 2 | 8 |
| α-helix | 22-23 | 2 | |
| β-strand | 30-36 | 7 | 9 |
| β-strand | 38-46 | 9 | 9 |
| β-strand | 51-54 | 4 | 9 |
| α-helix | 56-58 | 3 | |
| β-strand | 60-60A | 2 | 10 |
| α-helix | 60B-60D | 3 | |
| β-strand | 60F-60G | 2 | 10 |
| β-strand | 64-68 | 5 | 9 |
| β-strand | 72 | 1 | 11 |
| β-strand | 81-90 | 10 | 9 |
| β-strand | 104-108 | 5 | 9 |
| α-helix | 120-121 | 2 | |
| β-strand | 122 | 1 | 8 |
| α-helix | 123-125 | 3 | |
| α-helix | 128-129C | 5 | |
| β-strand | 135-139 | 5 | 8 |
| β-strand | 154 | 1 | 11 |
| β-strand | 156-162 | 7 | 8 |
| α-helix | 165-171 | 7 | |
| α-helix | 175-176 | 2 | |
| 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 | 235-241 | 7 | |
Chain L: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| α-helix | 14C-14I | 7 | |
Chain R: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 413-414 | 2 | 12 |
| β-strand | 421-422 | 2 | 12 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Alpha-thrombin (small subunit) | J, L | protein | 27 | Homo sapiens | P00734 (AlphaFold model) |
| Alpha-thrombin (large subunit) | H, K | protein | 259 | Homo sapiens | P00734 (AlphaFold model) |
| Thrombomodulin | R | protein | 19 | Homo sapiens | P07204 (AlphaFold model) |
Sequence of entity 1 (J, L), FASTA
>1HLT_1 ALPHA-THROMBIN (SMALL SUBUNIT) (chains J, L)
ADCGLRPLFEKKSLEDKTERELLESYI
Sequence of entity 2 (H, K), FASTA
>1HLT_2 ALPHA-THROMBIN (LARGE SUBUNIT) (chains H, K)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
Sequence of entity 3 (R), FASTA
>1HLT_3 Thrombomodulin (chains R)
ECPEGYILDDGFICTDIDE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 0G6 | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexa… | C21 H34 Cl N6 O3 | 2 |
Primary citation
Structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin complexed with thrombin. Mathews, I.I., Padmanabhan, K.P., Tulinksy, A. et al. Biochemistry (1994) 33:13547-13552. DOI 10.1021/bi00250a006 · 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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