1LDK: Cullin homolog
Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 8 May 2002.
- Method
- X-ray diffraction
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 7,922
- Mol. weight
- 118.91 kDa
- Ligands
- ZN
- Released
- 8 May 2002
Explore 1LDK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1LDK contains 48 α-helices and 16 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 A: 20 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-30 | 10 | |
| α-helix | 39-52 | 14 | |
| α-helix | 86-101 | 16 | |
| α-helix | 114-141 | 28 | |
| α-helix | 160-167 | 8 | |
| α-helix | 171-175 | 5 | |
| α-helix | 176-188 | 13 | |
| α-helix | 197-210 | 14 | |
| α-helix | 227 | 1 | |
| α-helix | 228-233 | 6 | |
| α-helix | 234-254 | 21 | |
| α-helix | 257-277 | 21 | |
| α-helix | 281-283 | 3 | |
| α-helix | 285-292 | 8 | |
| α-helix | 293-297 | 5 | |
| α-helix | 300-312 | 13 | |
| α-helix | 316-325 | 10 | |
| α-helix | 334-355 | 22 | |
| α-helix | 363-383 | 21 | |
| α-helix | 389-399 | 11 | |
Chain B: 15 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 418-430 | 13 | |
| α-helix | 439-453 | 15 | |
| α-helix | 461-475 | 15 | |
| α-helix | 482-493 | 12 | |
| α-helix | 500-526 | 27 | |
| β-strand | 537-540 | 4 | 1 |
| α-helix | 563-571 | 9 | |
| β-strand | 577-581 | 5 | 1 |
| β-strand | 587-589 | 3 | 2 |
| β-strand | 602-604 | 3 | 2 |
| α-helix | 605-610 | 6 | |
| β-strand | 620-621 | 2 | 3 |
| α-helix | 622-626 | 5 | |
| α-helix | 633-645 | 13 | |
| β-strand | 668-669 | 2 | 3 |
| α-helix | 691-700 | 10 | |
| α-helix | 702-710 | 9 | |
| α-helix | 716-719 | 4 | |
| β-strand | 726 | 1 | 4 |
| α-helix | 727-730 | 4 | |
| α-helix | 753-756 | 4 | |
| α-helix | 757-759 | 3 | |
| β-strand | 771 | 1 | 4 |
Chain C: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1026-1027 | 2 | 2 |
| β-strand | 1029-1035 | 7 | 1 |
| α-helix | 1055-1058 | 4 | |
| β-strand | 1070-1071 | 2 | 5 |
| β-strand | 1079-1080 | 2 | 5 |
| α-helix | 1094 | 1 | |
Chain D: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2004 | 1 | 6 |
| β-strand | 2008 | 1 | 7 |
| β-strand | 2016 | 1 | 6 |
| α-helix | 2018-2021 | 4 | |
| α-helix | 2025-2029 | 5 | |
| β-strand | 2041 | 1 | 7 |
| α-helix | 2046-2058 | 13 | |
| α-helix | 2088-2092 | 5 | |
| α-helix | 2097-2109 | 13 | |
| α-helix | 2113-2125 | 13 | |
| α-helix | 2132-2139 | 8 | |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3114-3120 | 7 | |
| α-helix | 3126-3128 | 3 | |
| α-helix | 3129-3132 | 4 | |
| α-helix | 3137-3143 | 7 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin homolog | A | protein | 396 | Homo sapiens | Q13616 (AlphaFold model) |
| Cullin homolog | B | protein | 366 | Homo sapiens | Q13616 (AlphaFold model) |
| ring-box protein 1 | C | protein | 90 | Homo sapiens | P62877 (AlphaFold model) |
| Cyclin A/CDK2-associated protein P19 | D | protein | 133 | Homo sapiens | P63208 (AlphaFold model) |
| SKP2-like protein type gamma | E | protein | 41 | Homo sapiens | Q13309 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>1LDK_1 CULLIN HOMOLOG (chains A)
IGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKK
GQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLN
GICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGE
TINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQ
NPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLDAD
KNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLDVH
KKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTK
Sequence of entity 2 (B), FASTA
>1LDK_2 CULLIN HOMOLOG (chains B)
MAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKML
AKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEP
LDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGEL
VTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLV
LEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLL
IQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKD
TYSYLA
Sequence of entity 3 (C), FASTA
>1LDK_3 ring-box protein 1 (chains C)
KKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHA
FHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 4 (D), FASTA
>1LDK_4 CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 (chains D)
PSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHKD
DPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMI
KGKTPEEIRKTFN
Sequence of entity 5 (E), FASTA
>1LDK_5 SKP2-like protein type gamma (chains E)
WDSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLW
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
Primary citation
Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex. Zheng, N., Schulman, B.A., Song, L. et al. Nature (2002) 416:703-709. DOI 10.1038/416703a · PubMed
Other PDB entries of the same protein (UniProt Q13616 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
- 5V89 1.55 Å, Structure of DCN4 PONY domain bound to CUL1 WHB
- 3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
- 8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
- 7Z8R 2.7 Å, CAND1-CUL1-RBX1
- 7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
- 8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
- 9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
- 1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
- 4F52 3.0 Å, Structure of a Glomulin-RBX1-CUL1 complex
- 7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked
- 9XZL 3.0 Å, Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex…
Browse structure collections
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