4YDY: Darpin 44C12V5

Crystal structure of darpin 44C12V5 in complex with human il-4. Determined by X-ray diffraction at 2.0 Å resolution. Released 4 Mar 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: synthetic construct, Homo sapiens
Chains: 4
Atoms: 4,625
Mol. weight: 66.26 kDa
Released: 4 Mar 2015

Explore 4YDY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YDY contains 37 α-helices and 4 β-strands across 4 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 and B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	13-24	12
α-helix	27-36	10
α-helix	50-56	7
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9
α-helix	149-155	7
α-helix	159-166	8

Chain I: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	5-19	15
α-helix	23-26	4
β-strand	28-30	3	1
α-helix	32-35	4
α-helix	41-60	20
α-helix	75-89	15
α-helix	91-94	4
β-strand	106-108	3	1
α-helix	109-124	16
α-helix	125-128	4

Chain J: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-19	16
α-helix	23-26	4
β-strand	28-30	3	2
α-helix	32-35	4
α-helix	41-59	19
α-helix	63-66	4
α-helix	71-89	19
α-helix	91-94	4
β-strand	106-108	3	2
α-helix	109-125	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Darpin 44C12V5	A, B	protein	169	synthetic construct
Interleukin-4	I, J	protein	130	Homo sapiens	P05112 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4YDY_1 DARPIN 44C12V5 (chains A, B)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNALDDSGYTPLHLAAEDGHL
EIVEVLLKHGADVNAADRLGDTPLHLAAFVGHLEIVEVLLKAGADVNAVDLAGVTPLHVA
AFYGHLEIVEVLLKAGADVNAQDKFGKTPADIAADNGHEDIAEVLQKLN

Sequence of entity 2 (I, J), FASTA

>4YDY_2 Interleukin-4 (chains I, J)
MHKCDITLQEIIKTLNSLTEQKTLCTELTVTDIFAASKNTTEKETFCRAATVLRQFYSHH
EKDTRCLGATAQQFHRHKQLIRFLKRLDRNLWGLAGLNSCPVKEANQSTLENFLERLKTI
MREKYSKCSS

Primary citation

CRYSTAL STRUCTURE OF DARPIN 44C12V5 IN COMPLEX WITH HUMAN IL-4. Teplyakov, A., Obmolova, G., Gilliland, G. To be published.

Other PDB entries of the same protein (UniProt P05112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2D48 1.65 Å, Crystal structure of the Interleukin-4 variant T13D
2B8X 1.7 Å, Crystal structure of the interleukin-4 variant F82D
2B8U 1.8 Å, Crystal structure of wildtype human Interleukin-4
2B8Y 1.8 Å, Crystal structure of the interleukin-4 variant T13DF82D
2B91 2.0 Å, Crystal structure of the interleukin-4 variant F82DR85A
1HZI 2.05 Å, Interleukin-4 mutant E9A
2B90 2.1 Å, Crystal structure of the interleukin-4 variant T13DR85A
1RCB 2.25 Å, Crystal structure of human recombinant interleukin-4 at 2.25 Å resolution
1IAR 2.3 Å, Interleukin-4 / receptor alpha chain complex
2INT 2.35 Å, Crystal structure of recombinant human interleukin-4
2B8Z 2.5 Å, Crystal structure of the interleukin-4 variant R85A
5FHX 2.55 Å, Crystal structure of codv in complex with IL4 at 2.55 ang. Resolution.

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