6SQS: Cat phospho-Ser429 MDM2 RING domain

Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub. Determined by X-ray diffraction at 1.83 Å resolution. Released 6 May 2020.

Method: X-ray diffraction
Resolution: 1.83 Å
Organisms: Felis catus, Homo sapiens
Chains: 6
Atoms: 4,711
Mol. weight: 65.61 kDa
Ligands: ZN
Released: 6 May 2020

Explore 6SQS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SQS contains 27 α-helices and 42 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	455-457	3	1
α-helix	462-470	9
β-strand	484-489	6	1

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-25	5	2
β-strand	32-38	7	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	75	1	3
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	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain C: 4 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
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5
β-strand	75	1	4

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	432-435	4
β-strand	437	1	7
β-strand	445	1	7
β-strand	448-452	5	1
β-strand	455-457	3	1
α-helix	462-470	9
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	8
β-strand	29-38	10	8
α-helix	39-40	2
β-strand	49-55	7	8
α-helix	64-65	2
β-strand	66-69	4	8
β-strand	75	1	9
β-strand	78	1	9
β-strand	83	1	8
β-strand	84	1	9
β-strand	86	1	10
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-146	16

Chain F: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	11
β-strand	12-17	6	11
β-strand	22	1	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	11
α-helix	48	1
β-strand	49	1	11
α-helix	50-51	2
β-strand	55	1	12
α-helix	57-59	3
β-strand	66-71	6	11
β-strand	75	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A, D	protein	64	Felis catus	Q7YRZ8 (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

>6SQS_1 E3 ubiquitin-protein ligase Mdm2 (chains A, D)
PSFPHNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVL
TYFP

Sequence of entity 2 (B, E), FASTA

>6SQS_2 Ubiquitin-conjugating enzyme E2 D2 (chains B, E)
ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 3 (C, F), FASTA

>6SQS_3 Ubiquitin-40S ribosomal protein S27a (chains C, F)
SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY
NIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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 Q7YRZ8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6SQP 1.21 Å, Crystal structure of Cat MDM2-S429E RING domain homodimer
6SQR 2.18 Å, Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub

Browse structure collections

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