Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites. Determined by X-ray diffraction at 3.2 Å resolution. Released 1 Jun 2011.
Explore 3PMH in 3D Show helices and sheets RCSB PDB PDBe
3PMH contains 20 α-helices and 39 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 |
|---|---|---|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14G | 5 | |
| α-helix | 14H-14J | 3 |
| 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 | 39-48 | 10 | 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 | 81-90 | 10 | 3 |
| β-strand | 95 | 1 | 6 |
| β-strand | 100 | 1 | 6 |
| β-strand | 104-108 | 5 | 3 |
| α-helix | 120-121 | 2 | |
| β-strand | 122 | 1 | 2 |
| α-helix | 123-124 | 2 | |
| α-helix | 126-129C | 7 | |
| β-strand | 135-140 | 6 | 2 |
| β-strand | 154 | 1 | 5 |
| β-strand | 156-163 | 8 | 2 |
| α-helix | 164 | 1 | |
| α-helix | 165-169 | 5 | |
| 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 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 5-7 | 3 | 7 |
| β-strand | 13-16 | 4 | 7 |
| β-strand | 33-37 | 5 | 7 |
| β-strand | 45-47 | 3 | 8 |
| α-helix | 48-51 | 4 | |
| β-strand | 59-61 | 3 | 7 |
| β-strand | 69-71 | 3 | 8 |
| β-strand | 81-83 | 3 | 7 |
| β-strand | 104-106 | 3 | 7 |
| β-strand | 128-130 | 3 | 7 |
| β-strand | 152-154 | 3 | 7 |
| β-strand | 176-178 | 3 | 7 |
| β-strand | 199-201 | 3 | 7 |
| β-strand | 207 | 1 | 9 |
| α-helix | 215-222 | 8 | |
| α-helix | 224-226 | 3 | |
| β-strand | 227 | 1 | 7 |
| α-helix | 243-245 | 3 | |
| β-strand | 247 | 1 | 10 |
| β-strand | 248 | 1 | 9 |
| β-strand | 255 | 1 | 10 |
| α-helix | 256-258 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Thrombin alpha-chain | A | protein | 36 | Homo sapiens | P00734 (AlphaFold model) |
| Thrombin beta-chain | B | protein | 259 | Homo sapiens | P00734 (AlphaFold model) |
| Platelet glycoprotein Ib alpha chain | G | protein | 290 | Homo sapiens | P07359 (AlphaFold model) |
>3PMH_1 THROMBIN ALPHA-CHAIN (chains A) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>3PMH_2 THROMBIN BETA-CHAIN (chains B) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>3PMH_3 Platelet glycoprotein Ib alpha chain (chains G) HPICEVSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQL NLDRAELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGAL RGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQ ENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMT SNVASVQCDNSDKFPVYKYPGKGCPTLGDEGDTDLYDYYPEEDTEGDKVR
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| 0G7 | D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide | C21 H31 Cl N6 O3 | 1 |
Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I. Zarpellon, A., Celikel, R., Roberts, J.R. et al. Proc Natl Acad Sci U S A (2011) 108:8628-8633. DOI 10.1073/pnas.1017042108 · PubMed
Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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