7DR4: PDB entry 7DR4

Complex of anti-human IL-2 antibody and human IL-2. Determined by X-ray diffraction at 2.49 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 2.49 Å
Organisms: Mus musculus, Homo sapiens
Chains: 12
Atoms: 17,347
Mol. weight: 252.25 kDa
Released: 14 Apr 2021

Explore 7DR4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DR4 contains 86 α-helices and 182 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.

Chain A: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
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	45-52	8	12
β-strand	57-60	4	12
β-strand	65	1	11
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	108-111	4	12
β-strand	115-119	5	12
α-helix	122-124	3
β-strand	125	1	13
β-strand	128-132	5	14
β-strand	143-153	11	14
β-strand	154	1	13
β-strand	159-162	4	15
α-helix	163-165	3
β-strand	171-173	3	14
α-helix	174-176	3
β-strand	177-179	3	14
β-strand	182-192	11	14
β-strand	201-206	6	15
β-strand	214-218	5	15

Chain B: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-65	4	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	96	1
β-strand	97-98	2	17
β-strand	102-106	5	17
β-strand	111	1	18
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-125	4
β-strand	132-139	8	19
β-strand	140	1	18
β-strand	144-145	2	20
β-strand	160-163	4	19
α-helix	164-167	4
β-strand	173-179	7	19
β-strand	197-198	2	20

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	21
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	29-31	3
α-helix	33	1
β-strand	34-39	6	22
β-strand	45-52	8	22
β-strand	57-60	4	22
α-helix	62-65	4
β-strand	68-73	6	21
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-99	8	22
β-strand	108-111	4	22
β-strand	115-119	5	22
β-strand	125	1	23
α-helix	126-127	2
β-strand	128-132	5	24
β-strand	143-153	11	24
β-strand	154	1	23
β-strand	159-162	4	25
α-helix	163-165	3
β-strand	171-173	3	24
α-helix	174-176	3
β-strand	177-179	3	24
β-strand	182-192	11	24
β-strand	202-207	6	25
α-helix	208-210	3
β-strand	212-217	6	25

Chain D: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-13	4	27
α-helix	17-18	2
β-strand	19-29	11	26
β-strand	33-38	6	27
α-helix	43-44	2
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-66	5	26
β-strand	68-75	8	26
α-helix	80-82	3
β-strand	84-90	7	27
α-helix	96	1
β-strand	97-98	2	27
β-strand	102-106	5	27
β-strand	111	1	28
β-strand	114-118	5	29
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	144-150	7	30
β-strand	153-155	3	30
β-strand	159-163	5	29
α-helix	164-167	4
β-strand	173-182	10	29
α-helix	183-188	6
β-strand	191-198	8	30
β-strand	205-210	6	30

Chain E: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	31
α-helix	7	1
β-strand	10-12	3	32
β-strand	18-25	8	31
α-helix	29-31	3
β-strand	34-39	6	32
β-strand	45-52	8	32
β-strand	57-60	4	32
α-helix	62-64	3
β-strand	65	1	31
β-strand	68-73	6	31
β-strand	78-83	6	31
α-helix	88-90	3
β-strand	92-99	8	32
β-strand	108-111	4	32
β-strand	115-119	5	32
β-strand	125	1	33
β-strand	128-132	5	34
β-strand	143-153	11	34
β-strand	154	1	33
β-strand	159-162	4	35
β-strand	171-173	3	34
α-helix	174-176	3
β-strand	177-178	2	34
β-strand	183-192	10	34
β-strand	202-207	6	35
α-helix	208-210	3
β-strand	212-217	6	35

Chain F: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	10-13	4	37
α-helix	18	1
β-strand	19-29	11	36
β-strand	33-38	6	37
β-strand	45-49	5	37
β-strand	53-54	2	37
α-helix	55	1
β-strand	62-65	4	36
β-strand	68-75	8	36
β-strand	84-90	7	37
α-helix	96	1
β-strand	97-98	2	37
β-strand	102-106	5	37
β-strand	111	1	38
β-strand	114-118	5	39
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	39
β-strand	140	1	38
β-strand	144-150	7	40
β-strand	153-155	3	40
β-strand	159-163	5	39
α-helix	164-167	4
β-strand	173-182	10	39
α-helix	183-188	6
β-strand	191-198	8	40
β-strand	201-210	10	40

Chain G: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
α-helix	36-39	4
β-strand	44-47	4	41
α-helix	53-56	4
α-helix	57-60	4
α-helix	63-73	11
α-helix	82-97	16
β-strand	107-112	6	41
α-helix	114-131	18

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-52	8	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	65	1	1
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	108-111	4	2
β-strand	115-119	5	2
α-helix	123-124	2
β-strand	125	1	3
α-helix	126-127	2
β-strand	128-132	5	4
α-helix	138-140	3
β-strand	143-153	11	4
β-strand	154	1	3
β-strand	159-162	4	5
β-strand	167	1	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	177-179	3	4
β-strand	182-192	11	4
α-helix	193-195	3
β-strand	201-207	7	5
β-strand	212-218	7	5

4 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
anti-human IL-2 antibody, mouse Ig G, heavy chain	A, C, E, H	protein	224	Mus musculus
anti-human IL-2 antibody, mouse Ig G, kappa chain	B, D, F, L	protein	214	Mus musculus
Interleukin-2	G, I, J, K	protein	133	Homo sapiens	P60568 (AlphaFold model)

Sequence of entity 1 (A, C, E, H), FASTA

>7DR4_1 anti-human IL-2 antibody, mouse Ig G, heavy chain (chains A, C, E, H)
EVQLQQSGAELARPGASVKLSCKASGYTFTTYWIQWVKQRPGQGLEWIGAIYPGDGDTRY
IQNFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARSLATRGFYAMDYWGQGTSVTVS
SAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT

Sequence of entity 2 (B, D, F, L), FASTA

>7DR4_2 anti-human IL-2 antibody, mouse Ig G, kappa chain (chains B, D, F, L)
DIVMTQSPASLSMAIGEKVTIRCITSTDIDDDMNWYQQKPGEPPKLLISEGNTLRPGVPS
RFSSSGYGTDFVFTIENMLSEDVADYYCLQSDNLPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (G, I, J, K), FASTA

>7DR4_3 Interleukin-2 (chains G, I, J, K)
APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLE
EELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNR
WITFCQSIISTLT

Primary citation

Crystal structure of human interleukin-2 in complex with TCB2, a new antibody-drug candidate with antitumor activity. Kim, J., Lee, J.Y., Park, S.Y. et al. Oncoimmunology (2021) 10:1899671-1899671. DOI 10.1080/2162402X.2021.1899671 · PubMed

Other PDB entries of the same protein (UniProt P60568 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SOZ 1.64 Å, Structure of the complex formed by human interleukin-2 and scFv 602
8SOW 1.71 Å, Structure of the complex formed by human interleukin-2 and scFv F10
7M2G 1.79 Å, INTERLEUKIN-2 (human) mutant P65K, C125S
4NEJ 1.92 Å, Small molecular fragment bound to crystal contact interface of Interleukin-2
4NEM 1.93 Å, Small molecular fragment bound to crystal contact interface of Interleukin-2
1M48 1.95 Å, Crystal Structure of Human IL-2 Complexed with (R)-N-[2-[1-(Aminoiminomethyl)-3-piperidin…
5LQB 1.95 Å, Complex structure of human IL2 mutant, Proleukin, with Fab fragment of NARA1 antibody
1M47 1.99 Å, Crystal Structure of Human Interleukin-2
1M49 2.0 Å, Crystal Structure of Human Interleukin-2 Complexed with SP-1985
1M4B 2.15 Å, Crystal Structure of Human Interleukin-2 K43C Covalently Modified at C43 with…
1M4A 2.18 Å, Crystal Structure of Human Interleukin-2 Y31C Covalently Modified at C31 with…
1NBP 2.2 Å, Crystal Structure Of Human Interleukin-2 Y31C Covalently Modified At C31 With…

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