3EYC: New crystal structure of human tear lipocalin

New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21. Determined by X-ray diffraction at 2.6 Å resolution. Released 6 Oct 2009.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,524
Mol. weight: 72.16 kDa
Ligands: BU1
Released: 6 Oct 2009

Explore 3EYC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EYC contains 12 α-helices and 52 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.

Chain A: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15-17	3	1
β-strand	18-24	7	2
α-helix	25	1
β-strand	33-36	4	1
β-strand	39-43	5	1
α-helix	44	1
β-strand	49-57	9	1
β-strand	60-68	9	1
β-strand	69-70	2	2
β-strand	76-79	4	2
β-strand	84-90	7	2
β-strand	96-105	10	2
β-strand	108-117	10	2
α-helix	124-136	13
β-strand	143-146	4	2
α-helix	147-148	2
β-strand	149	1	1

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15-17	3	3
β-strand	18-24	7	4
α-helix	25	1
β-strand	33-36	4	3
β-strand	39-43	5	3
β-strand	49-57	9	3
β-strand	60-68	9	3
β-strand	69-70	2	4
β-strand	76-79	4	4
β-strand	84-90	7	4
β-strand	96-105	10	4
β-strand	108-117	10	4
α-helix	124-136	13
β-strand	143-145	3	4
α-helix	147	1
β-strand	148-149	2	3

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15-17	3	5
β-strand	18-23	6	2
β-strand	33-36	4	5
β-strand	39-43	5	5
β-strand	49-57	9	5
β-strand	60-68	9	5
β-strand	69-70	2	2
β-strand	76-79	4	2
β-strand	84-90	7	2
β-strand	96-103	8	2
β-strand	110-117	8	2
α-helix	124-136	13
β-strand	144-146	3	2
α-helix	147	1
β-strand	148-149	2	5

Chain D: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15-17	3	6
β-strand	18-24	7	7
α-helix	25	1
β-strand	33-36	4	6
β-strand	39-43	5	6
β-strand	49-57	9	6
β-strand	60-68	9	6
β-strand	69	1	7
β-strand	76-79	4	7
β-strand	84-90	7	7
β-strand	96-104	9	7
β-strand	109-117	9	7
α-helix	124-136	13
β-strand	143-145	3	7
α-helix	147	1
β-strand	148-149	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipocalin-1	A, B, C, D	protein	162	Homo sapiens	P31025 (AlphaFold model)

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

>3EYC_1 Lipocalin-1 (chains A, B, C, D)
ASDEEIQDVSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEV
KAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYSEGELHGKPVRGVKLVGRDPKNNL
EALEDFEKAAGARGLSTESILIPRQSETCSPGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
BU1	1,4-butanediol	C4 H10 O2	4

Primary citation

A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity. Breustedt, D.A., Chatwell, L., Skerra, A. Acta Crystallogr D Biol Crystallogr (2009) 65:1118-1125. DOI 10.1107/S0907444909031011 · PubMed

Other PDB entries of the same protein (UniProt P31025 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1XKI 1.8 Å, Crystal structure of human tear lipocalin/von Ebners gland protein
4QAF 1.8 Å, Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)
5T43 NMR Structure of Apo-form Human Tear Lipocalin

Browse structure collections

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