6MVD: Lecithin:cholesterol acyltransferase

Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in complex with isopropyl dodec-11-enylfluorophosphonate (IDFP) and a small molecule activator. Determined by X-ray diffraction at 3.1 Å resolution. Released 5 Dec 2018.

Method
X-ray diffraction
Resolution
3.1 Å
Organism
Homo sapiens
Chains
2
Atoms
6,181
Mol. weight
90.38 kDa
Ligands
NI, H94, H9A, NAG
Released
5 Dec 2018

Explore 6MVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MVD contains 36 α-helices and 55 β-strands across 2 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: 18 helices, 27 β-strands

ElementResiduesLengthSheet
α-helix22-243
β-strand25-2841
β-strand36-4052
β-strand4113
β-strand5313
β-strand58-6142
α-helix64-663
α-helix71-799
β-strand81-8444
β-strand89-9244
β-strand96-9942
α-helix107-1104
β-strand11115
β-strand11915
α-helix122-1298
β-strand13511
β-strand139-14131
α-helix150-1523
α-helix154-17118
β-strand175-18061
α-helix182-19211
α-helix196-2027
β-strand203-20971
α-helix218-2258
β-strand22716
β-strand23216
β-strand23417
α-helix242-2443
β-strand24617
β-strand264-26748
β-strand272-27438
α-helix278-2847
α-helix288-29710
β-strand311-31771
β-strand319-32688
α-helix335-3362
β-strand338-34478
β-strand34918
α-helix350-3534
α-helix355-3595
β-strand36019
β-strand36319
β-strand367-37371
α-helix377-3793
α-helix384-39411
Chain B: 18 helices, 28 β-strands
ElementResiduesLengthSheet
β-strand25-28410
β-strand36-40511
β-strand41112
β-strand53112
β-strand58-61411
α-helix64-674
α-helix71-799
β-strand81113
β-strand82-84314
β-strand89-91314
α-helix92-932
β-strand96-99411
α-helix107-1104
β-strand111115
β-strand119115
α-helix122-1298
β-strand135110
β-strand139-141310
α-helix154-17118
α-helix1741
β-strand175-180610
α-helix182-19312
α-helix196-2027
β-strand203-209710
α-helix218-2258
β-strand227-228216
β-strand231-232216
β-strand234113
β-strand246113
β-strand264-267417
β-strand272-274317
α-helix275-2773
α-helix278-2847
α-helix288-29811
β-strand311-317710
β-strand319-327917
α-helix3351
β-strand336-344917
β-strand349117
α-helix350-3534
α-helix354-3596
β-strand360118
β-strand363118
β-strand367-373710
α-helix379-3813
α-helix384-39411

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Phosphatidylcholine-sterol acyltransferaseA, Bprotein383Homo sapiensP04180 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>6MVD_1 Phosphatidylcholine-sterol acyltransferase (chains A, B)
HTRPVILVPGCLGNQLEAKLDKPDVVNWMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTR
VVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGYLHTLVQNLVNNGYVRDETVR
AAPYDWRLEPGQQEEYYRKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLLRQPQAWKD
RFIDGFISLGAPWGGSIKPMLVLASGDNQGIPIMSSIKLKEEQRITTTSPWMFPSRMAWP
EDHVFISTPSFNYTGRDFQRFFADLHFEEGWYMWLQSRDLLAGLPAPGVEVYCLYGVGLP
TPRTYIYDHGFPYTDPVGVLYEDGDDTVATRSTELCGLWQGRQPQPVHLLPLHGIQHLNM
VFSNLTLEHINAILLGAHHHHHH

Ligands and cofactors

IDNameFormulaCopies
NINickel (II) ionNi1
H946-{4-[(4R)-4-hydroxy-6-oxo-4-(trifluoromethyl)-4,5,6,7-tetrahydro-2H-pyrazolo[3…C19 H16 F6 N6 O22
H9Apropan-2-yl hydrogen (R)-ethylphosphonateC5 H13 O3 P2
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O65

Water and common crystallization additives (SO4) are not listed.

Primary citation

Molecular basis for activation of lecithin:cholesterol acyltransferase by a compound that increases HDL cholesterol. Manthei, K.A., Yang, S.M., Baljinnyam, B. et al. Elife (2018) 7. DOI 10.7554/eLife.41604 · PubMed

Other PDB entries of the same protein (UniProt P04180 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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