6GB6: H-2Kb with dipeptide GL

Structure of H-2Kb with dipeptide GL. Determined by X-ray diffraction at 1.78 Å resolution. Released 6 Mar 2019.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,719
Mol. weight: 88.05 kDa
Ligands: GLY, LEU
Released: 6 Mar 2019

Explore 6GB6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GB6 contains 23 α-helices and 60 β-strands across 4 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
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	52-54	3
α-helix	57-85	29
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	138-148	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-170	6
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	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

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
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
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 D: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	5
α-helix	20	1
β-strand	21-28	8	5
β-strand	31-37	7	5
β-strand	46-47	2	5
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	5
β-strand	109-118	10	5
β-strand	121-126	6	5
β-strand	133-135	3	5
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-179	16
β-strand	183	1	6
α-helix	184-185	2
β-strand	186-193	8	7
β-strand	198-208	11	7
β-strand	209	1	6
β-strand	214-219	6	8
β-strand	222-223	2	8
β-strand	229-230	2	7
α-helix	231-233	3
β-strand	234-235	2	7
β-strand	241-250	10	7
α-helix	254-256	3
β-strand	257-262	6	8
β-strand	270-272	3	8

Chain E: 1 helix, 11 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, K-B alpha chain	A, D	protein	276	Mus musculus	P01901 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Mus musculus	P01887 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6GB6_1 H-2 class I histocompatibility antigen, K-B alpha chain (chains A, D)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEP

Sequence of entity 2 (B, E), FASTA

>6GB6_2 Beta-2-microglobulin (chains B, E)
GIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	2
LEU	Leucine	C6 H13 N O2	2

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

Primary citation

Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin. Hafstrand, I., Sayitoglu, E.C., Apavaloaei, A. et al. Proc Natl Acad Sci U S A (2019) 116:5055-5060. DOI 10.1073/pnas.1807656116 · PubMed

Other PDB entries of the same protein (UniProt P01901 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LK2 1.35 Å, 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
1G7P 1.5 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
1KPU 1.5 Å, High resolution crystal structure of the MHC class I complex H-2Kb/VSV8
1G7Q 1.6 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
3TID 1.65 Å, Crystal structure of the LCMV derived peptide GP34 in complex with the murine mhc class…
1FZK 1.7 Å, MHC class I natural mutant H-2KBM1 heavy chain complexed with beta-2 microglobulin and…
1KPV 1.71 Å, High resolution crystal structure of the MHC class I complex H-2Kb/SEV9
1LEG 1.75 Å, Crystal Structure of H-2Kb bound to the dEV8 peptide
1FZM 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1FZO 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1T0N 1.8 Å, Conformational switch in polymorphic H-2K molecules containing an HSV peptide
2QRT 1.8 Å, Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy…

Browse structure collections

About this viewer

MolViewer shows 6GB6 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.