2VYR: Human MDM4 N-terminal domain

Structure of human MDM4 N-terminal domain bound to a single domain antibody. Determined by X-ray diffraction at 2.0 Å resolution. Released 25 Nov 2008.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 12
Atoms: 11,261
Mol. weight: 181.94 kDa
Released: 25 Nov 2008

Explore 2VYR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VYR contains 44 α-helices and 117 β-strands across 12 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.

Chains A, B and D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	1
α-helix	31-39	9
β-strand	47	1	1
α-helix	49-62	14
β-strand	66-67	2	2
β-strand	70-75	6	2
α-helix	80-85	6
β-strand	89-91	3	2
α-helix	96-105	10
β-strand	106-108	3	1

Chain C: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	5
α-helix	31-39	9
β-strand	47	1	5
α-helix	49-62	14
β-strand	66	1	6
β-strand	73-75	3	6
α-helix	80-85	6
β-strand	89-91	3	6
α-helix	96-105	10
β-strand	106-108	3	5

Chain E: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
α-helix	44-45	2
β-strand	46-51	6	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	113-114	2	10
β-strand	118-122	5	10

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	46-51	6	12
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	113-114	2	12
β-strand	118-122	5	12

Chain G: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11-12	2	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	46-51	6	15
β-strand	58-60	3	15
α-helix	62-64	3
β-strand	68-73	6	13
α-helix	74-76	3
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-98	7	15
β-strand	113-114	2	15
β-strand	118-120	3	15
β-strand	121-122	2	14

Chain H: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	11-12	2	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	46-51	6	18
β-strand	58-60	3	18
β-strand	65	1	16
β-strand	68-73	6	16
α-helix	74-76	3
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-98	7	18
β-strand	113-114	2	18
β-strand	118-120	3	18
β-strand	121-122	2	17

Chain I: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	45-51	7	20
β-strand	58-60	3	20
β-strand	68-73	6	19
α-helix	74-76	3
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-99	8	20
α-helix	109-110	2
β-strand	111-114	4	20
β-strand	118-122	5	20

Chain J: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-40	7	22
β-strand	44-51	8	22
β-strand	58-60	3	22
α-helix	62-64	3
β-strand	68-73	6	21
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-99	8	22
α-helix	109-110	2
β-strand	111-114	4	22
β-strand	118-122	5	22

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MDM4 protein	A, B, C, D	protein	101	HOMO SAPIENS	O15151 (AlphaFold model)
Human single domain antibody	E, F, G, H, I, J, K, L	protein	153	HOMO SAPIENS

Sequence of entity 1 (A, B, C, D), FASTA

>2VYR_1 MDM4 PROTEIN (chains A, B, C, D)
ACRISPGQINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVY
CGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLATATTDA

Sequence of entity 2 (E, F, G, H, I, J, K, L), FASTA

>2VYR_2 HUMAN SINGLE DOMAIN ANTIBODY (chains E, F, G, H, I, J, K, L)
EVQLLESGGGLVQPGGSLRLSCAASGFTFEEYAMLWVRQAPGKGLEWVSGINARGYTTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYYCAKPWYPFMASKGSEFDYWGQGTLV
TVSSAAALEIKRASQPELAPEDPEDVEHHHHHH

Primary citation

Structure of Human Mdm4 N-Terminal Domain Bound to a Single-Domain Antibody. Yu, G.W., Vaysburd, M., Allen, M.D. et al. J Mol Biol (2009) 385:1578. DOI 10.1016/J.JMB.2008.11.043 · PubMed

Other PDB entries of the same protein (UniProt O15151 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q9Y 1.2 Å, HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; Structural states of Hdm2 and…
3FEA 1.33 Å, Crystal Structure of HdmX bound to the p53-peptidomimetic…
3FE7 1.35 Å, Crystal Structure of HdmX bound to the p53-peptidomimetic…
3FDO 1.4 Å, Structure of human MDMX in complex with high affinity peptide
3LBJ 1.5 Å, Structure of human MDMX protein in complex with a small molecule inhibitor
4RXZ 1.55 Å, Crystal Structure of MDMX phosporylated Tyr99 in complex with a 12-mer peptide
6Q9W 1.55 Å, X-ray structure of compound 15 bound to HdmX: Structural states of Hdm2 and HdmX: X-ray…
3EQY 1.63 Å, Crystal structure of human MDMX in complex with a 12-mer peptide inhibitor
7C3Y 1.63 Å, Crystal structure of the N-terminal domain of human MdmX protein in complex with Nutlin3a
7C44 1.65 Å, Crystal structure of the p53-binding domain of human MdmX protein in complex with Nutlin3a
8HDG 1.73 Å, Small peptide enhances the binding of nutline-3a to MdmX
3JZP 1.74 Å, Human MDMX liganded with a 12mer peptide inhibitor (pDI6W)

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