5OCK: ACPA E4

Crystal structure of ACPA E4 in complex with CEP1. Determined by X-ray diffraction at 1.6 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,007
Mol. weight: 49.48 kDa
Released: 4 Jul 2018

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

Secondary structure: helices and β-sheets

5OCK contains 17 α-helices and 50 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: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	15
β-strand	12	1	11
α-helix	14-16	3
β-strand	17-18	2	15

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
β-strand	34-40	7	10
β-strand	46-52	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-100	9	10
β-strand	102	1	11
β-strand	106-110	5	10
β-strand	114-116	3	10
β-strand	117-118	2	9
α-helix	122-123	2
β-strand	124	1	12
α-helix	125-126	2
β-strand	127-131	5	13
α-helix	133-134	2
α-helix	137-139	3
β-strand	142-152	11	13
β-strand	153	1	12
β-strand	158-163	6	14
β-strand	170-172	3	13
α-helix	173-175	3
β-strand	176-178	3	13
β-strand	181-191	11	13
β-strand	200-206	7	14
α-helix	207-209	3
β-strand	211-216	6	14

Chain L: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-12	4	3
β-strand	18-23	6	2
β-strand	35-39	5	3
β-strand	46-49	4	3
β-strand	50	1	4
β-strand	54	1	4
β-strand	63-67	5	2
β-strand	71-76	6	2
α-helix	81-83	3
β-strand	85-93	9	3
β-strand	98-101	4	3
β-strand	102	1	1
β-strand	105-109	5	3
α-helix	110	1
β-strand	114	1	5
α-helix	115-116	2
β-strand	117-121	5	6
α-helix	122-124	3
α-helix	125-129	5
β-strand	132-142	11	6
β-strand	143	1	5
β-strand	148-153	6	7
β-strand	156-158	3	7
β-strand	162-166	5	6
α-helix	167-170	4
β-strand	176-185	10	6
α-helix	186-190	5
β-strand	194-200	7	7
α-helix	207	1
β-strand	208-213	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human ACPA E4 Fab fragment - Light chain	L	protein	217	Homo sapiens
Human ACPA E4 Fab fragment - Heavy chain	H	protein	221	Homo sapiens
CEP1 peptide (from enolase)	A	protein	21	Homo sapiens	P06733 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>5OCK_1 Human ACPA E4 Fab fragment - Light chain (chains L)
QSVWTQPPSVSAAPGQKVTISCSGDDSILRSAFVSWYQQVPGSAPKLVIFDDRQRPSGIP
ARFSGSNSGTTATLDIAGLQRGDEADYYCAAWNGRLSAFVFGSGTKLEIKRADAAPTVSI
FPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSS
TLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>5OCK_2 Human ACPA E4 Fab fragment - Heavy chain (chains H)
QVQLEESGPGLVRPSETLSLSCTVSGFPMSESYFWGWIRQSPGKGLEWLGSVIHTGTTYY
RPSLESRLTIAMDPSKNQVSLSLTSVTVADSAMYYCVRIRGGSSNWLDPWGPGIVVTASS
AKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSG
LYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPRP

Sequence of entity 3 (A), FASTA

>5OCK_3 CEP1 peptide (from enolase) (chains A)
XCKIHAREIFDSRGNPTVECK

Primary citation

Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies. Ge, C., Xu, B., Liang, B. et al. Arthritis Rheumatol (2019) 71:210-221. DOI 10.1002/art.40698 · PubMed

Other PDB entries of the same protein (UniProt P06733 (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
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
5JLZ 1.99 Å, Crystal structure of HLA-DRB1*04:01 in complex with modified alpha-enolase peptide 26-40…
2PSN 2.2 Å, Crystal structure of enolase1
3B97 2.2 Å, Crystal Structure of human Enolase 1
8TRL 2.4 Å, T cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4
5LAX 2.6 Å, Crystal structure of HLA_DRB1*04:01 in complex with alpha-enolase peptide 26-40
9X4F 2.7 Å, Crystal structure of tetrameric alpha-enolase with asymmetric flexible active sites
9A0U Docking model of HLA class I with HLA class II

Browse structure collections

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