5KNM: PDB entry 5KNM

Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with NK-cell receptors. Determined by X-ray diffraction at 3.3 Å resolution. Released 14 Jun 2017.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, Trichoplusia ni
Chains: 4
Atoms: 4,528
Mol. weight: 83.36 kDa
Ligands: NAG
Released: 14 Jun 2017

Explore 5KNM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KNM contains 17 α-helices and 48 β-strands across 3 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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	45-47	3	1
α-helix	50-52	3
α-helix	57-82	26
β-strand	94-103	10	1
β-strand	109	1	1
β-strand	113-118	6	1
β-strand	124-126	3	1
β-strand	133-135	3	1
α-helix	140-150	11
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-195	10	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-223	2	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-263	7	4
β-strand	270-272	3	4

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
α-helix	14-15	2
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
α-helix	90	1
β-strand	91-94	4	7

Chain D: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	8
β-strand	15-17	3	9
β-strand	23-27	5	8
β-strand	35-39	5	10
α-helix	43-44	2
α-helix	52-55	4
β-strand	60	1	8
α-helix	67-69	3
β-strand	71-72	2	11
β-strand	73-77	5	10
β-strand	88	1	10
β-strand	92-93	2	11
β-strand	94-96	3	9
α-helix	100-102	3
β-strand	103-104	2	12
β-strand	121-123	3	12
β-strand	130-134	5	13
β-strand	144-147	4	13
β-strand	156-158	3	12
β-strand	173-177	5	13
β-strand	184-185	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen,…	A	protein	284	Homo sapiens	P30511 (AlphaFold model)
Beta-2-microglobulin	B	protein	182	Homo sapiens	P61769 (AlphaFold model)
Leukocyte immunoglobulin-like receptor subfamily B member 1	D	protein	267	Homo sapiens	Q8NHL6 (AlphaFold model)
Peptide ILE-LEU-ARG-TRP-GLU-GLN	N	protein	6	Trichoplusia ni

Sequence of entity 1 (A), FASTA

>5KNM_1 cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F (chains A)
GSHSLRYFSTAVSRPGRGEPRYIAVEYVDDTQFLRFDSDAAIPRMEPREPWVEQEGPQYW
EWTTGYAKANAQTDRVALRNLLRRYNQSEAGSHTLQGMNGCDMGPDGRLLRGYHQHAYDG
KDYISLNEDLRSWTAADTVAQITQRFYEAEEYAEEFRTYLEGECLELLRRYLENGKETLQ
RADPPKAHVAHHPISDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPQPLILRWEQSPQPTIPI

Sequence of entity 2 (B), FASTA

>5KNM_2 Beta-2-microglobulin (chains B)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADLHHHHHHHHGSGGLEVLFQG
PEFGGSADPIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEH
SDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGSGSGG
GS

Sequence of entity 3 (D), FASTA

>5KNM_3 Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains D)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADLHHHHHHHHGSGGLEVLFQG
PEFGGSADLGHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIP
QELVKKGQFPIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPV
VNSGGNVILQCDSQVAFDGFSLCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWW
YRCYAYDSNSPYEWSLPSDLLELLVLG

Sequence of entity 4 (N), FASTA

>5KNM_4 Peptide ILE-LEU-ARG-TRP-GLU-GLN (chains N)
ILRWEQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Human Leukocyte Antigen F Presents Peptides and Regulates Immunity through Interactions with NK Cell Receptors. Dulberger, C.L., McMurtrey, C.P., Holzemer, A. et al. Immunity (2017) 46:1018-1029.e7. DOI 10.1016/j.immuni.2017.06.002 · PubMed

Other PDB entries of the same protein (UniProt P30511 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IUE 2.62 Å, Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through…

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