6SQO: Human MDM2 RING domain homodimer
Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub. Determined by X-ray diffraction at 1.41 Å resolution. Released 6 May 2020.
- Method
- X-ray diffraction
- Resolution
- 1.41 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 5,181
- Mol. weight
- 65.14 kDa
- Ligands
- ZN
- Released
- 6 May 2020
Explore 6SQO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6SQO contains 24 α-helices and 39 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: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 432-435 | 4 | |
| β-strand | 448-452 | 5 | 1 |
| β-strand | 455-460 | 6 | 1 |
| α-helix | 462-470 | 9 | |
| β-strand | 484-489 | 6 | 1 |
Chain B: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| β-strand | 21-26 | 6 | 2 |
| β-strand | 29-38 | 10 | 2 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 2 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 2 |
| β-strand | 78 | 1 | 3 |
| β-strand | 83 | 1 | 2 |
| β-strand | 84 | 1 | 3 |
| β-strand | 86 | 1 | 4 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-110 | 12 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain C: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 5 |
| β-strand | 12-17 | 6 | 5 |
| β-strand | 22 | 1 | 6 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 5 |
| β-strand | 48-49 | 2 | 5 |
| β-strand | 55 | 1 | 6 |
| β-strand | 66-71 | 6 | 5 |
| β-strand | 75 | 1 | 4 |
Chain D: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 432-435 | 4 | |
| β-strand | 448-452 | 5 | 1 |
| β-strand | 455-460 | 6 | 1 |
| α-helix | 462-470 | 9 | |
| α-helix | 473-475 | 3 | |
| β-strand | 484-489 | 6 | 1 |
Chain E: 7 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| β-strand | 21-26 | 6 | 7 |
| β-strand | 29-38 | 10 | 7 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 7 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 7 |
| β-strand | 75 | 1 | 8 |
| β-strand | 78 | 1 | 8 |
| β-strand | 83 | 1 | 7 |
| β-strand | 84 | 1 | 8 |
| β-strand | 86 | 1 | 9 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-110 | 12 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain F: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 10 |
| β-strand | 12-17 | 6 | 10 |
| β-strand | 22 | 1 | 11 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 10 |
| β-strand | 48-49 | 2 | 10 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 11 |
| β-strand | 66-71 | 6 | 10 |
| β-strand | 75 | 1 | 9 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| E3 ubiquitin-protein ligase Mdm2 | A, D | protein | 62 | Homo sapiens | Q00987 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 D2 | B, E | protein | 146 | Homo sapiens | P62837 (AlphaFold model) |
| Ubiquitin-40S ribosomal protein S27a | C, F | protein | 77 | Homo sapiens | P62979 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>6SQO_1 E3 ubiquitin-protein ligase Mdm2 (chains A, D)
LPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTY
FP
Sequence of entity 2 (B, E), FASTA
>6SQO_2 Ubiquitin-conjugating enzyme E2 D2 (chains B, E)
ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM
Sequence of entity 3 (C, F), FASTA
>6SQO_3 Ubiquitin-40S ribosomal protein S27a (chains C, F)
SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY
NIQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Water and common crystallization additives (NO3, CL) are not listed.
Primary citation
Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain. Magnussen, H.M., Ahmed, S.F., Sibbet, G.J. et al. Nat Commun (2020) 11:2094-2094. DOI 10.1038/s41467-020-15783-y · PubMed
Other PDB entries of the same protein (UniProt Q00987 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6Q9L 1.13 Å, HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2…
- 5C5A 1.15 Å, Crystal Structure of HDM2 in complex with Nutlin-3a
- 6Q9O 1.21 Å, HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; Structural states of Hdm2…
- 5ZXF 1.25 Å, The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a
- 7QDQ 1.26 Å, Crystal Structure of HDM2 in complex with Caylin-1
- 8F10 1.28 Å, Structure of the MDM2 P53 binding domain in complex with H102, an all-D Helicon…
- 8P0D 1.31 Å, Human 14-3-3 sigma in complex with human MDM2 peptide
- 5Z02 1.35 Å, Crystal structure of HIS6-tagged Mdm2 with nutlin-3a
- 8J81 1.35 Å, MDM2 bound with a peptoid
- 4OGN 1.38 Å, Co-Crystal Structure of MDM2 with Inhbitor Compound 3
- 2AXI 1.4 Å, HDM2 in complex with a beta-hairpin
- 7KJM 1.4 Å, Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-omega)
Browse structure collections
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