5VK0

Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
CSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
ESCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
GSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
ISCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
KSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
MSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
OSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
QSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
SSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
USCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)
WSCOP2B SuperfamilySWIB/MDM2 domain-like8037458 3000287 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF02201e5vk0A1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
CPF02201e5vk0C1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
EPF02201e5vk0E1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
GPF02201e5vk0G1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
IPF02201e5vk0I1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
KPF02201e5vk0K1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
MPF02201e5vk0M1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
OPF02201e5vk0O1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
QPF02201e5vk0Q1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
SPF02201e5vk0S1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
UPF02201e5vk0U1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)
WPF02201e5vk0W1 A: alpha arraysX: SWIB/MDM2 domain (From Topology)H: SWIB/MDM2 domain (From Topology)T: SWIB/MDM2 domainF: PF02201ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
C1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
E1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
G1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
I1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
K1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
M1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
O1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
Q1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
S1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
U1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)
W1.10.245.10 Mainly Alpha Orthogonal Bundle MDM2 SWIB/MDM2 domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, C, E, G, I
PF02201SWIB/MDM2 domain (SWIB)SWIB/MDM2 domainThis family includes the SWIB domain and the MDM2 domain [1]. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. Thi ...This family includes the SWIB domain and the MDM2 domain [1]. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2 [2].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, C, E, G, I
E3 ubiquitin-protein ligase Mdm2
B, D, F, H, J
Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, C, E, G, I
IPR003121SWIB/MDM2 domainDomain
A, C, E, G, I
IPR016495p53 negative regulator Mdm2/Mdm4Family
A, C, E, G, I
IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
A, C, E, G, I
IPR001876Zinc finger, RanBP2-typeDomain
A, C, E, G, I
IPR036443Zinc finger, RanBP2-type superfamilyHomologous Superfamily
A, C, E, G, I
IPR036885SWIB/MDM2 domain superfamilyHomologous Superfamily
A, C, E, G, I
IPR044080MDM2, modified RING finger, HC subclassDomain
A, C, E, G, I
IPR001841Zinc finger, RING-typeDomain
A, C, E, G, I
IPR028340E3 ubiquitin-protein ligase Mdm2Family

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
B, D, F, H, J
9E7 Parent Component: LYS

B, D, F, H, J
ACE RESIDAA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

PSI-MOD :  N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
B, D, F, H, J
NH2 RESIDAA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100

PSI-MOD :  N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109