5NIR: Collagen 2A vWC domain

Crystal structure of collagen 2A vWC domain. Determined by X-ray diffraction at 1.74 Å resolution. Released 14 Jun 2017.

Method: X-ray diffraction
Resolution: 1.74 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,233
Mol. weight: 18.57 kDa
Ligands: P33
Released: 14 Jun 2017

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

Secondary structure: helices and β-sheets

5NIR contains 0 α-helices and 17 β-strands across 2 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: 0 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	34-36	3	1
β-strand	39-41	3	1
β-strand	46-50	5	2
β-strand	53-58	6	2
β-strand	61-70	10	2
β-strand	79	1	3
β-strand	88-89	2	3
β-strand	97	1	4

Chain B: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	34-36	3	5
β-strand	39-41	3	5
β-strand	46-50	5	2
β-strand	53-58	6	2
β-strand	61-69	9	2
β-strand	71-72	2	3
β-strand	74	1	4
β-strand	79	1	6
β-strand	88	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagen alpha-1(II) chain	A, B	protein	74	Homo sapiens	P02458 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5NIR_1 Collagen alpha-1(II) chain (chains A, B)
GSMAQEAGSCVQDGQRYNDKDVWKPEPCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGE
CCPICPTDLATASG

Ligands and cofactors

ID	Name	Formula	Copies
P33	3,6,9,12,15,18-hexaoxaicosane-1,20-diol	C14 H30 O8	1

Water and common crystallization additives (PG4, PEG, EDO) are not listed.

Primary citation

Structural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2. Xu, E.R., Blythe, E.E., Fischer, G. et al. J Biol Chem (2017) 292:12516-12527. DOI 10.1074/jbc.M117.788992 · PubMed

Other PDB entries of the same protein (UniProt P02458 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HG7 1.0 Å, Crystal structure of a collagen II fragment containing the binding site of PEDF and…
5OCX 1.75 Å, Crystal structure of ACPA E4 in complex with CII-C-13-CIT
7NZE 2.05 Å, Crystal structure of HLA-DR4 in complex with a human collagen type II peptide
6NIX 2.1 Å, Crystal structure of Immune Receptor
2SEB 2.5 Å, X-ray crystal structure of HLA-DR4 complexed with a peptide from human collagen II
6BIN 2.5 Å, HLA-DRB1 in complex with Type II collagen peptide
5OCY 2.6 Å, Crystal structure of ACPA E4 in complex with CII-C-48-CIT
5MV4 2.9 Å, ACC1 Fab fragment in complex with citrullinated CII616-639 epitope of collagen type II…
2FSE 3.1 Å, Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1…
1U5M Structure of a Chordin-like Cysteine-rich Repeat (VWC module) from Collagen IIA

Browse structure collections

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