1ICF: MHC class II associated P41 II fragment

Crystal structure of MHC class II associated P41 II fragment in complex with cathepsin L. Determined by X-ray diffraction at 2.0 Å resolution. Released 12 Jan 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,060
Mol. weight: 62.72 kDa
Ligands: NAG
Released: 12 Jan 2000

Explore 1ICF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ICF contains 30 α-helices and 52 β-strands across 6 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 C: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	14-16	3
β-strand	18	1	2
β-strand	23	1	3
α-helix	25-42	18
β-strand	48	1	4
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	3
α-helix	70-80	11
β-strand	83-84	2	5
β-strand	85	1	4
α-helix	102-104	3
β-strand	105-107	3	5
β-strand	111-114	4	1
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	1
α-helix	141-144	4
β-strand	150-151	2	1
β-strand	161	1	6
β-strand	163-172	10	1

Chains B and D: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	181-186	6	1
β-strand	189	1	2
β-strand	195	1	1
β-strand	198-202	5	1
α-helix	208-210	3
β-strand	216-219	4	1

Chains I and J: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	196-201	6
β-strand	207	1	6
β-strand	216	1	13
α-helix	221	1
β-strand	222	1	13
α-helix	223	1
β-strand	225-228	4	14
β-strand	233-236	4	14
β-strand	237	1	15
α-helix	242	1
β-strand	243	1	15
α-helix	244	1
β-strand	249	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (cathepsin L: heavy chain)	A, C	protein	175	Homo sapiens	P07711 (AlphaFold model)
Protein (cathepsin L: light chain)	B, D	protein	42	Homo sapiens	P07711 (AlphaFold model)
Protein (invariant chain)	I, J	protein	65	Homo sapiens	P04233 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1ICF_1 PROTEIN (CATHEPSIN L: HEAVY CHAIN) (chains A, C)
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ
GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEK
ALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFEST

Sequence of entity 2 (B, D), FASTA

>1ICF_2 PROTEIN (CATHEPSIN L: LIGHT CHAIN) (chains B, D)
NNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Sequence of entity 3 (I, J), FASTA

>1ICF_3 PROTEIN (INVARIANT CHAIN) (chains I, J)
LTKCQEEVSHIPAVHPGSFRPKCDENGNYLPLQCYGSIGYCWCVFPNGTEVPNTRSRGHH
NCSES

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. Guncar, G., Pungercic, G., Klemencic, I. et al. EMBO J (1999) 18:793-803. DOI 10.1093/emboj/18.4.793 · PubMed

Other PDB entries of the same protein (UniProt P07711 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XU3 0.9 Å, Cathepsin L with a nitrile inhibitor
5MAE 1.0 Å, CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro…
5MAJ 1.0 Å, CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morp…
2XU4 1.12 Å, Cathepsin L with a nitrile inhibitor
5MQY 1.13 Å, CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluorop…
2YJC 1.14 Å, Cathepsin L with a nitrile inhibitor
2YJ2 1.15 Å, Cathepsin L with a nitrile inhibitor
3HHA 1.27 Å, Crystal structure of cathepsin L in complex with AZ12878478
2YJ8 1.3 Å, Cathepsin L with a nitrile inhibitor
2YJ9 1.35 Å, Cathepsin L with a nitrile inhibitor
7Z58 1.35 Å, Crystal structure of human Cathepsin L in complex with covalently bound Calpeptin
6EZP 1.37 Å, CATHEPSIN L IN COMPLEX WITH (3S,14E)-19-chloro-N-(1-cyanocyclopropyl)-5-oxo-12,17-dioxa-4…

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