3OV6: CD1c

CD1c in complex with MPM (mannosyl-beta1-phosphomycoketide). Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Jan 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,126
Mol. weight: 45.61 kDa
Ligands: NAG, D12, MK0
Released: 19 Jan 2011

Explore 3OV6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3OV6 contains 13 α-helices and 30 β-strands across 1 chain. 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: 13 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	1003	1	1
α-helix	1004-1005	2
β-strand	1006-1011	6	2
β-strand	1021-1030	10	2
β-strand	1031	1	1
β-strand	1035-1041	7	3
β-strand	1044-1045	2	3
β-strand	1050-1051	2	2
α-helix	1052-1054	3
β-strand	1055-1056	2	2
β-strand	1062-1070	9	2
β-strand	1078-1084	7	3
β-strand	1091-1095	5	3
α-helix	1097-1099	3
β-strand	7-18	12	4
β-strand	24-32	9	4
β-strand	35-41	7	4
β-strand	46-49	4	4
α-helix	60-82	23
β-strand	94-105	12	4
β-strand	110-118	9	4
β-strand	121-127	7	4
β-strand	130-133	4	4
α-helix	134	1
α-helix	139-146	8
α-helix	147-151	5
α-helix	155-161	7
α-helix	162-166	5
α-helix	167-181	15
β-strand	186	1	5
β-strand	189-194	6	6
β-strand	202-212	11	6
β-strand	213	1	5
β-strand	218-223	6	7
β-strand	226-227	2	7
β-strand	232-233	2	6
β-strand	237-238	2	6
α-helix	239	1
β-strand	244-253	10	6
α-helix	254-256	3
β-strand	260-265	6	7
α-helix	267-269	3
β-strand	274-277	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin, T-cell surface glycoprotein CD1c, T-cell surface glycoprotein CD1b	A	protein	397	Homo sapiens	P29016 (AlphaFold model), P29017 (AlphaFold model), P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3OV6_1 Beta-2-microglobulin, T-cell surface glycoprotein CD1c,  T-cell surface glycoprotein CD1b (chains A)
ADPIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGSGSGGGSSADA
SQEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHQWSKGQFSNEEL
SDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGGSPEGFFQVAFNGLDL
LSFQQTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKMYVH
RQVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNAQGT
WYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
D12	Dodecane	C12 H26	1
MK0	1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosph…	C38 H77 O9 P	1

Primary citation

The 2.5 A structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. Scharf, L., Li, N.S., Hawk, A.J. et al. Immunity (2010) 33:853-862. DOI 10.1016/j.immuni.2010.11.026 · PubMed

Other PDB entries of the same protein (UniProt P29016 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WL1 1.38 Å, Crystal Structure of Human CD1b in Complex with PG
8GLG 1.6 Å, Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1
5L2J 1.65 Å, Crystal Structure of human CD1b in complex with C36-GMM
5WKE 1.69 Å, Crystal Structure of Human CD1b in Complex with PS
6D64 1.7 Å, Crystal Structure of Human CD1b in Complex with POPC
7MX4 1.73 Å, CD1c with antigen analogue 1
2H26 1.8 Å, human CD1b in complex with endogenous phosphatidylcholine and spacer
8GLH 1.83 Å, Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5
9OI0 1.84 Å, Crystal structure of CD1b presenting ganglioside GD3
8GLE 1.85 Å, Crystal Structure of Human CD1b in Complex with Lysosulfatide
3T8X 1.9 Å, Crystal structure of human CD1b in complex with synthetic antigenic…
8DV3 1.9 Å, Crystal structure of human CD1b presenting Phosphatidylinositol C34:1

Browse structure collections

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