5WLI: H-2Db with the GAP501 peptide

Crystal Structure of H-2Db with the GAP501 peptide (SQL). Determined by X-ray diffraction at 2.2 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Mus musculus, Plasmodium berghei
Chains: 12
Atoms: 13,917
Mol. weight: 180.25 kDa
Ligands: PO4
Released: 15 Nov 2017

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

Secondary structure: helices and β-sheets

5WLI contains 53 α-helices and 120 β-strands across 8 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
α-helix	87-88	2
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	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-194	9	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-224	3	4
β-strand	229-230	2	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

Chains B and H: 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	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
β-strand	91-94	4	7

Chain D: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	8
α-helix	19-20	2
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-54	5
α-helix	57-84	28
α-helix	87-88	2
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-224	3	11
β-strand	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chains E and K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain G: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	15
α-helix	19-20	2
β-strand	21-28	8	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	50-54	5
α-helix	57-84	28
α-helix	87-88	2
β-strand	93-103	11	15
β-strand	109-118	10	15
β-strand	121-126	6	15
β-strand	133-135	3	15
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	16
α-helix	184-185	2
β-strand	186-193	8	17
β-strand	198-208	11	17
β-strand	209	1	16
β-strand	214-219	6	18
β-strand	222-224	3	18
β-strand	229-230	2	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-250	10	17
α-helix	254-256	3
β-strand	257-262	6	18
β-strand	270-272	3	18

Chain J: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	22
α-helix	18-20	3
β-strand	21-28	8	22
β-strand	31-37	7	22
β-strand	46-47	2	22
α-helix	50-54	5
α-helix	57-84	28
α-helix	87-88	2
β-strand	93-103	11	22
β-strand	109-118	10	22
β-strand	121-126	6	22
β-strand	133-135	3	22
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	23
β-strand	186-193	8	24
β-strand	198-208	11	24
β-strand	209	1	23
β-strand	214-219	6	25
β-strand	222-224	3	25
β-strand	229-230	2	24
α-helix	231-233	3
β-strand	234-235	2	24
β-strand	241-250	10	24
α-helix	254-256	3
β-strand	257-262	6	25
β-strand	270-272	3	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A, D, G, J	protein	278	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B, E, H, K	protein	99	Mus musculus	P01887 (AlphaFold model)
GAP50 peptide	C, F, I, L	protein	9	Plasmodium berghei	A0A0Y9W4B5 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>5WLI_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, D, G, J)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPP

Sequence of entity 2 (B, E, H, K), FASTA

>5WLI_2 Beta-2-microglobulin (chains B, E, H, K)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (C, F, I, L), FASTA

>5WLI_3 GAP50 peptide (chains C, F, I, L)
SQLLNAKYL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3

Primary citation

A T Cell Receptor Locus Harbors a Malaria-Specific Immune Response Gene. Van Braeckel-Budimir, N., Gras, S., Ladell, K. et al. Immunity (2017) 47:835-847.e4. DOI 10.1016/j.immuni.2017.10.013 · PubMed

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…

Browse structure collections

About this viewer

MolViewer shows 5WLI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.