5MK3: PDB entry 5MK3
Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro 1 domain (CHMP4C peptide complex structure). Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Aug 2017.
- Method
- X-ray diffraction
- Resolution
- 2.0 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 12,582
- Mol. weight
- 171.24 kDa
- Released
- 16 Aug 2017
Explore 5MK3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5MK3 contains 83 α-helices and 12 β-strands across 8 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: 20 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| α-helix | 13-16 | 4 | |
| β-strand | 17 | 1 | 1 |
| α-helix | 22-29 | 8 | |
| α-helix | 30-34 | 5 | |
| α-helix | 38-41 | 4 | |
| α-helix | 42-56 | 15 | |
| α-helix | 62-81 | 20 | |
| β-strand | 94-97 | 4 | 1 |
| β-strand | 104-107 | 4 | 1 |
| α-helix | 110-131 | 22 | |
| α-helix | 137-160 | 24 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-195 | 25 | |
| α-helix | 200-222 | 23 | |
| α-helix | 224-230 | 7 | |
| α-helix | 232-262 | 31 | |
| α-helix | 266-286 | 21 | |
| α-helix | 292-315 | 24 | |
| α-helix | 316-320 | 5 | |
| α-helix | 331-335 | 5 | |
| α-helix | 342-344 | 3 | |
| α-helix | 349-352 | 4 | |
Chain B: 20 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| α-helix | 13-16 | 4 | |
| β-strand | 17 | 1 | 2 |
| α-helix | 23-33 | 11 | |
| α-helix | 38-41 | 4 | |
| α-helix | 42-56 | 15 | |
| α-helix | 62-81 | 20 | |
| β-strand | 94-97 | 4 | 2 |
| β-strand | 104-107 | 4 | 2 |
| α-helix | 110-131 | 22 | |
| α-helix | 137-160 | 24 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-196 | 26 | |
| α-helix | 200-221 | 22 | |
| α-helix | 224-230 | 7 | |
| α-helix | 232-262 | 31 | |
| α-helix | 266-286 | 21 | |
| α-helix | 292-315 | 24 | |
| α-helix | 316-320 | 5 | |
| α-helix | 327-329 | 3 | |
| α-helix | 332-335 | 4 | |
| α-helix | 341-344 | 4 | |
| α-helix | 349-352 | 4 | |
Chain C: 20 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| α-helix | 13-16 | 4 | |
| β-strand | 17-20 | 4 | 3 |
| α-helix | 22-32 | 11 | |
| α-helix | 38-41 | 4 | |
| α-helix | 42-56 | 15 | |
| α-helix | 62-81 | 20 | |
| β-strand | 94-97 | 4 | 3 |
| β-strand | 104-107 | 4 | 3 |
| α-helix | 110-131 | 22 | |
| α-helix | 137-160 | 24 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-195 | 25 | |
| α-helix | 200-221 | 22 | |
| α-helix | 224-230 | 7 | |
| α-helix | 232-262 | 31 | |
| α-helix | 266-286 | 21 | |
| α-helix | 292-315 | 24 | |
| α-helix | 316-320 | 5 | |
| α-helix | 327-329 | 3 | |
| α-helix | 332-335 | 4 | |
| α-helix | 341-343 | 3 | |
| α-helix | 349-352 | 4 | |
Chain D: 19 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| α-helix | 13-16 | 4 | |
| β-strand | 17-20 | 4 | 4 |
| α-helix | 23-32 | 10 | |
| α-helix | 38-41 | 4 | |
| α-helix | 42-56 | 15 | |
| α-helix | 62-81 | 20 | |
| β-strand | 94-97 | 4 | 4 |
| β-strand | 104-107 | 4 | 4 |
| α-helix | 110-131 | 22 | |
| α-helix | 137-160 | 24 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-195 | 25 | |
| α-helix | 200-221 | 22 | |
| α-helix | 224-230 | 7 | |
| α-helix | 232-262 | 31 | |
| α-helix | 266-286 | 21 | |
| α-helix | 292-315 | 24 | |
| α-helix | 316-320 | 5 | |
| α-helix | 331-335 | 5 | |
| α-helix | 341-343 | 3 | |
| α-helix | 349-352 | 4 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-13 | 9 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-28 | 9 | |
Chain G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-39 | 8 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-53 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Tyrosine-protein phosphatase non-receptor type 23 | A, B, C, D | protein | 361 | Homo sapiens | Q9H3S7 (AlphaFold model) |
| Charged multivesicular body protein 4c | E, F, G, H | protein | 18 | Homo sapiens | Q96CF2 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>5MK3_1 Tyrosine-protein phosphatase non-receptor type 23 (chains A, B, C, D)
MEAVPRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPR
DFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYN
LGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNL
MLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKL
VQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRF
TMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKL
V
Sequence of entity 2 (E, F, G, H), FASTA
>5MK3_2 Charged multivesicular body protein 4c (chains E, F, G, H)
QRAEEEDDDIKQLAAWAT
Primary citation
Structural Basis for Specific Interaction of TGF beta Signaling Regulators SARA/Endofin with HD-PTP. Gahloth, D., Levy, C., Walker, L. et al. Structure (2017) 25:1011-1024.e4. DOI 10.1016/j.str.2017.05.005 · PubMed
Other PDB entries of the same protein (UniProt Q9H3S7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5MK2 1.7 Å, Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1…
- 5MK0 1.76 Å, Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1…
- 5MJZ 1.87 Å, Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1…
- 3RAU 1.95 Å, Crystal structure of the HD-PTP Bro1 domain
- 5CRV 2.0 Å, Crystal structure of the Bro domain of HD-PTP in a complex with the core region of STAM2
- 5MJY 2.25 Å, Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1…
- 5CRU 2.4 Å, Crystal structure of the Bro domain of HD-PTP
- 5MK1 2.5 Å, Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1…
- 5LM2 2.54 Å, Crystal Structure of HD-PTP phosphatase
- 5LM1 2.55 Å, Crystal Structure of HD-PTP phosphatase in complex with UBAP1
Browse structure collections
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