3EDR: Caspase-7
The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO. Determined by X-ray diffraction at 2.45 Å resolution. Released 28 Oct 2008.
- Method
- X-ray diffraction
- Resolution
- 2.45 Å
- Organisms
- Homo sapiens, Saccharomyces cerevisiae (Baker's yeast)
- Chains
- 6
- Atoms
- 3,943
- Mol. weight
- 63.01 kDa
- Released
- 28 Oct 2008
Explore 3EDR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3EDR contains 19 α-helices and 44 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: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 59 | 1 | 1 |
| β-strand | 66 | 1 | 2 |
| β-strand | 68-74 | 7 | 3 |
| α-helix | 80-82 | 3 | |
| α-helix | 84-86 | 3 | |
| α-helix | 90-104 | 15 | |
| β-strand | 106-112 | 7 | 3 |
| α-helix | 116-128 | 13 | |
| β-strand | 134 | 1 | 2 |
| β-strand | 137-142 | 6 | 3 |
| β-strand | 145-146 | 2 | 4 |
| β-strand | 149-152 | 4 | 4 |
| β-strand | 155-158 | 4 | 4 |
| α-helix | 159-164 | 6 | |
| α-helix | 168-170 | 3 | |
| α-helix | 172-174 | 3 | |
| β-strand | 179-184 | 6 | 3 |
| β-strand | 188-190 | 3 | 5 |
| β-strand | 192 | 1 | 6 |
| β-strand | 195 | 1 | 7 |
Chain B: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 213 | 1 | 8 |
| β-strand | 219-223 | 5 | 3 |
| β-strand | 228-229 | 2 | 5 |
| β-strand | 232-234 | 3 | 9 |
| β-strand | 238-239 | 2 | 9 |
| α-helix | 240-252 | 13 | |
| α-helix | 258-272 | 15 | |
| β-strand | 286 | 1 | 6 |
| β-strand | 290-293 | 4 | 3 |
| β-strand | 298 | 1 | 1 |
Chain C: 8 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-358 | 3 | |
| β-strand | 359 | 1 | 10 |
| β-strand | 366 | 1 | 11 |
| β-strand | 369-374 | 6 | 3 |
| α-helix | 380-382 | 3 | |
| α-helix | 384-386 | 3 | |
| α-helix | 390-404 | 15 | |
| β-strand | 407-412 | 6 | 3 |
| α-helix | 416-426 | 11 | |
| β-strand | 434 | 1 | 11 |
| β-strand | 437-442 | 6 | 3 |
| β-strand | 445-446 | 2 | 12 |
| β-strand | 449-451 | 3 | 12 |
| β-strand | 456-458 | 3 | 12 |
| α-helix | 459-463 | 5 | |
| α-helix | 464-466 | 3 | |
| α-helix | 472-474 | 3 | |
| β-strand | 479-484 | 6 | 3 |
| β-strand | 490 | 1 | 13 |
| β-strand | 492 | 1 | 14 |
| β-strand | 495 | 1 | 8 |
Chain D: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 513 | 1 | 7 |
| β-strand | 519-523 | 5 | 3 |
| β-strand | 529 | 1 | 13 |
| β-strand | 532-534 | 3 | 15 |
| β-strand | 538-539 | 2 | 15 |
| α-helix | 540-552 | 13 | |
| α-helix | 558-572 | 15 | |
| β-strand | 586 | 1 | 14 |
| β-strand | 590-593 | 4 | 3 |
| β-strand | 598 | 1 | 10 |
Chain E: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 704-705 | 2 | 9 |
Chain F: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 804-805 | 2 | 15 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Caspase-7 | A, C | protein | 173 | Homo sapiens | P55210 (AlphaFold model) |
| Caspase-7 | B, D | protein | 97 | Homo sapiens | P55210 (AlphaFold model) |
| Inhibitor Ac-ldesd-cho peptide | E, F | protein | 6 | Saccharomyces cerevisiae (Baker's yeast) | P36114 (AlphaFold model) |
Sequence of entity 1 (A, C), FASTA
>3EDR_1 Caspase-7 (chains A, C)
AKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTG
MGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLS
HGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ
Sequence of entity 2 (B, D), FASTA
>3EDR_2 Caspase-7 (chains B, D)
ANPRYKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVN
DRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ
Sequence of entity 3 (E, F), FASTA
>3EDR_3 Inhibitor Ac-ldesd-cho peptide (chains E, F)
XLDESX
Primary citation
Structural basis for executioner caspase recognition of P5 position in substrates. Fu, G., Chumanevich, A.A., Agniswamy, J. et al. Apoptosis (2008) 13:1291-1302. DOI 10.1007/s10495-008-0259-9 · PubMed
Other PDB entries of the same protein (UniProt P55210 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4JR2 1.65 Å, Human procaspase-7/caspase-7 heterodimer bound to Ac-DEVD-CMK
- 4JB8 1.7 Å, Caspase-7 in Complex with DARPin C7_16
- 2QL9 2.14 Å, Crystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO
- 4JR1 2.15 Å, Human procaspase-7 bound to Ac-DEVD-CMK
- 5K20 2.2 Å, Caspase-7 S239E Phosphomimetic
- 2QLB 2.25 Å, Crystal Structure of caspase-7 with inhibitor AC-ESMD-CHO
- 4LSZ 2.26 Å, Caspase-7 in Complex with DARPin D7.18
- 4ZVR 2.3 Å, Caspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to…
- 2QL5 2.34 Å, Crystal Structure of caspase-7 with inhibitor AC-DMQD-CHO
- 1F1J 2.35 Å, Crystal structure of caspase-7 in complex with acetyl-asp-glu-val-asp-cho
- 6CL2 2.35 Å, Caspase-7 in complex with Ac-ATS009-KE
- 1I4O 2.4 Å, Crystal structure of the xiap/caspase-7 complex
Browse structure collections
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