Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a). Determined by X-ray diffraction at 1.33 Å resolution. Released 7 Apr 2021.
Explore 6YHG in 3D Show helices and sheets RCSB PDB PDBe
6YHG contains 17 α-helices and 25 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.
| 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 | 81-83 | 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 | |
| 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 | 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 | 235-245 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 519-523 | 5 | |
| α-helix | 524-526 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14I | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Prothrombin | L | protein | 36 | Homo sapiens | P00734 (AlphaFold model) |
| Prothrombin | H | protein | 259 | Homo sapiens | P00734 (AlphaFold model) |
| Hirudin variant-2 | I | protein | 12 | Hirudo medicinalis | P09945 (AlphaFold model) |
>6YHG_1 Prothrombin (chains L) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>6YHG_2 Prothrombin (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>6YHG_3 Hirudin variant-2 (chains I) GDFEEIPEEYLQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| PRO | Proline | C5 H9 N O2 | 1 |
| DPN | D-phenylalanine | C9 H11 N O2 | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| PO4 | Phosphate ion | O4 P | 1 |
| SZ4 | 1-(3-methoxyphenyl)methanamine | C8 H11 N O | 1 |
Water and common crystallization additives (GOL, NA) are not listed.
Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a). Sandner, A., Heine, A., Klebe, G. To be published.
Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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