3S5L: CD4 mutant

Crystal structure of CD4 mutant bound to HLA-DR1. Determined by X-ray diffraction at 2.1 Å resolution. Released 21 Sept 2011.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Homo Sapiens
Chains: 8
Atoms: 9,272
Mol. weight: 133.88 kDa
Released: 21 Sept 2011

Explore 3S5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3S5L contains 31 α-helices and 104 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: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-50	5
β-strand	53	1	2
α-helix	57-76	20
α-helix	80-84	5
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-128	3	5
β-strand	133-134	2	4
α-helix	137	1
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	11
α-helix	96-97	2
β-strand	98-103	6	12
β-strand	114-122	9	12
β-strand	123	1	11
β-strand	128-133	6	13
β-strand	136-138	3	13
β-strand	142-144	3	12
β-strand	148-149	2	12
β-strand	155-162	8	12
β-strand	170-176	7	13
β-strand	184-189	6	13

Chains C and F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	2
α-helix	8-14	7

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	6
β-strand	19-26	8	6
β-strand	29-35	7	6
β-strand	40-43	4	6
α-helix	48-51	4
β-strand	53	1	7
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	8
α-helix	86-87	2
β-strand	88-93	6	9
β-strand	103-112	10	9
β-strand	113	1	8
β-strand	118-123	6	10
β-strand	126-127	2	10
β-strand	133-134	2	9
α-helix	137	1
β-strand	138-139	2	9
β-strand	145-153	9	9
β-strand	160-166	7	10
β-strand	174-179	6	10

Chain E: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	6
β-strand	23-32	10	6
β-strand	35-41	7	6
β-strand	47-49	3	6
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	14
α-helix	96-97	2
β-strand	98-103	6	15
β-strand	114-122	9	15
β-strand	123	1	14
β-strand	128-133	6	16
β-strand	136-138	3	16
β-strand	142-144	3	15
β-strand	148-149	2	15
β-strand	155-162	8	15
β-strand	170-176	7	16
β-strand	184-189	6	16

Chain G: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	12-14	3	17
β-strand	17	1	18
β-strand	26-29	4	12
β-strand	35-40	6	12
β-strand	43-46	4	12
β-strand	55-56	2	17
α-helix	59-62	4
β-strand	66	1	18
β-strand	69-71	3	17
α-helix	76-78	3
β-strand	80-86	7	12
β-strand	89-98	10	12
β-strand	99-102	4	19
β-strand	108	1	20
β-strand	114-119	6	19
β-strand	127-131	5	21
β-strand	137	1	21
β-strand	140	1	21
β-strand	143-146	4	19
α-helix	151-153	3
β-strand	155-163	9	21
β-strand	166-174	9	21
β-strand	176	1	20

Chain H: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	15
β-strand	12-14	3	22
β-strand	17	1	23
β-strand	26-29	4	15
β-strand	35-40	6	15
β-strand	43-46	4	15
β-strand	55-56	2	22
α-helix	59-62	4
β-strand	66	1	23
β-strand	69-71	3	22
α-helix	76-78	3
β-strand	80-86	7	15
β-strand	89-98	10	15
β-strand	99-101	3	24
β-strand	114	1	25
β-strand	117-119	3	24
β-strand	127-131	5	26
β-strand	137-140	4	26
β-strand	146	1	25
α-helix	151-153	3
β-strand	155-163	9	26
β-strand	166-174	9	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, D	protein	182	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen DR beta chain	B, E	protein	193	Homo sapiens	P01911 (AlphaFold model)
HA peptide	C, F	protein	13	Homo Sapiens	P03437
T-cell surface glycoprotein CD4	G, H	protein	191	Homo sapiens	P01730 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3S5L_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKQWEF
DA

Sequence of entity 2 (B, E), FASTA

>3S5L_2 HLA class II histocompatibility antigen DR beta chain (chains B, E)
MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAE
YWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSV
SGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPS
VTSPLTVEWRARS

Sequence of entity 3 (C, F), FASTA

>3S5L_3 HA peptide (chains C, F)
PKYVKQNTLKLAT

Sequence of entity 4 (G, H), FASTA

>3S5L_4 T-cell surface glycoprotein CD4 (chains G, H)
DLGSKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNYGSFLWKGPSKLNDRAD
SRRRLWRQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTL
TLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVV
LAAAAHHHHHH

Primary citation

Affinity maturation of human CD4 by yeast surface display and crystal structure of a CD4-HLA-DR1 complex. Wang, X.X., Li, Y., Yin, Y. et al. Proc Natl Acad Sci U S A (2011) 108:15960-15965. DOI 10.1073/pnas.1109438108 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

Browse structure collections

About this viewer

MolViewer shows 3S5L 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.