5B38: KIR3DL1*005

KIR3DL1*005 in complex with HLA-B*57:01. Determined by X-ray diffraction at 2.3 Å resolution. Released 30 Mar 2016.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,539
Mol. weight: 78.11 kDa
Ligands: NAG
Released: 30 Mar 2016

Explore 5B38 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B38 contains 21 α-helices and 63 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
α-helix	77	1
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain G: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	8
β-strand	17-19	3	9
β-strand	24-29	6	8
β-strand	37-40	4	10
β-strand	48	1	10
α-helix	49-52	4
β-strand	55	1	10
β-strand	59-61	3	8
α-helix	66-68	3
β-strand	70-72	3	11
β-strand	73-76	4	10
β-strand	77	1	12
β-strand	85	1	12
β-strand	92-94	3	11
β-strand	95-97	3	9
β-strand	104-108	5	13
β-strand	112-114	3	14
β-strand	119-125	7	13
β-strand	131-136	6	15
α-helix	142-143	2
β-strand	144-147	4	15
α-helix	148	1
β-strand	149-151	3	13
β-strand	154-161	8	13
α-helix	166-168	3
β-strand	170-177	8	15
β-strand	184	1	9
α-helix	187-191	5
β-strand	192-194	3	15
β-strand	195-197	3	14
α-helix	201-203	3
β-strand	204-207	4	16
β-strand	220-225	6	16
β-strand	231-236	6	17
β-strand	243-246	4	17
β-strand	248-249	2	16
β-strand	255-260	6	16
β-strand	268-275	8	17
β-strand	282-283	2	14
α-helix	285-289	5
β-strand	290-292	3	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, B-57 alpha chain	A	protein	276	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
peptide from Ig kappa chain C region	C	protein	9	Homo sapiens	P01834 (AlphaFold model)
Killer cell immunoglobulin-like receptor 3DL1	G	protein	299	Homo sapiens	P43629 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5B38_1 HLA class I histocompatibility antigen, B-57 alpha chain (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEYW
DGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>5B38_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>5B38_3 peptide from Ig kappa chain C region (chains C)
LSSPVTKSF

Sequence of entity 4 (G), FASTA

>5B38_4 Killer cell immunoglobulin-like receptor 3DL1 (chains G)
HMGGQDKPFLSAWPSAVVPRGGHVTLRCHYRHRFNNFMLYKEDRIHIPIFHGRIFQESFN
MSPVTTAHAGNYTCRGSHPHSPTGWSAPSNPVVIMVTGNHRKPSLLAHPGPLVKSGERVI
LQCWSDIMFEHFFLHKEGISKDPSRLVGQIHDGVSKANFSIGPMMLALAGTYRCYGSVTH
TSYQLSAPSDPLDIVVTGPYEKPSLSAQPGPKVQAGESVTLSCSSRSSYDMYHLSREGGA
HERRLPAVRKVNRTFQADFPLGPATHGGTYRCFGSFRHSPYELSDPSDPLLVSVTGNPS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Killer cell immunoglobulin-like receptor 3DL1 polymorphism defines distinct hierarchies of HLA class I recognition. Saunders, P.M., Pymm, P., Pietra, G. et al. J Exp Med (2016) 213:791-807. DOI 10.1084/jem.20152023 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide

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