1P53: ICAM-1 D3-D5 fragment

The Crystal Structure of ICAM-1 D3-D5 fragment. Determined by X-ray diffraction at 3.06 Å resolution. Released 4 May 2004.

Method: X-ray diffraction
Resolution: 3.06 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,955
Mol. weight: 58.99 kDa
Ligands: NAG
Released: 4 May 2004

Explore 1P53 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P53 contains 13 α-helices and 54 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: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	186	1	1
α-helix	191-192	2
β-strand	193-195	3	2
β-strand	199-201	3	3
β-strand	205-213	9	2
β-strand	216	1	1
α-helix	218-220	3
β-strand	222-227	6	3
β-strand	230-231	2	3
β-strand	235-239	5	2
β-strand	242-250	9	2
α-helix	253-255	3
β-strand	257-267	11	3
β-strand	270-281	12	3
β-strand	287-290	4	4
β-strand	294-296	3	5
β-strand	300-306	7	4
β-strand	326-332	7	4
α-helix	335-337	3
β-strand	341-350	10	6
β-strand	353-362	10	6
β-strand	364-366	3	5
β-strand	367-370	4	7
β-strand	379-383	5	8
β-strand	387-388	2	9
β-strand	395-397	3	7
β-strand	401-406	6	8
β-strand	410-411	2	8
β-strand	418-419	2	9
α-helix	422-424	3
β-strand	426-434	9	8
β-strand	437-448	12	8

Chain B: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	186	1	10
α-helix	191-192	2
β-strand	193-195	3	11
β-strand	199-201	3	12
β-strand	205-213	9	11
β-strand	216	1	10
α-helix	218-220	3
β-strand	222-227	6	12
β-strand	230-232	3	12
β-strand	235-239	5	11
β-strand	242-250	9	11
α-helix	253-255	3
β-strand	257-267	11	12
β-strand	270-281	12	12
β-strand	287-290	4	6
β-strand	294-296	3	13
β-strand	300-306	7	6
α-helix	325	1
β-strand	326-332	7	6
α-helix	335-337	3
β-strand	340-350	11	4
β-strand	353-363	11	4
β-strand	364-366	3	13
β-strand	367-370	4	14
β-strand	379-383	5	15
β-strand	387-388	2	16
β-strand	395-397	3	14
α-helix	399-400	2
β-strand	401-406	6	15
β-strand	410-411	2	15
α-helix	412	1
β-strand	418-419	2	16
α-helix	422-424	3
β-strand	426-434	9	15
β-strand	437-448	12	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Intercellular adhesion molecule-1	A, B	protein	266	Homo sapiens	P05362 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1P53_1 Intercellular adhesion molecule-1 (chains A, B)
FVLPATPPQLVSPRVLEVDTQGTVVCSLDGLFPVSEAQVHLALGDQRLNPTVTYGNDSFS
AKASVSVTAEDEGTQRLTCAVILGNQSQETLQTVTIYSFPAPNVILTKPEVSEGTEVTVK
CEAHPRAKVTLNGVPAQPLGPRAQLLLKATPEDNGRSFSCSATLEVAGQLIHKNQTRELR
VLYGPRLDERDCPGNWTWPENSQQTPMCQAWGNPLPELKCLKDGTFPLPIGESVTVTRDL
EGTYLCRARSTQGEVTREVTVNVLSP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Structural basis for dimerization of ICAM-1 on the cell surface. Yang, Y., Jun, C.D., Liu, J.H. et al. Mol Cell (2004) 14:269-276. DOI 10.1016/S1097-2765(04)00204-7 · PubMed

Other PDB entries of the same protein (UniProt P05362 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IAM 2.1 Å, Structure of the two amino-terminal domains of human intercellular adhesion molecule-1,…
7BG7 2.4 Å, HRV14 in complex with its receptor ICAM-1
2OZ4 2.7 Å, Structural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Surface Dimerization
5MZA 2.78 Å, The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1
1IC1 3.0 Å, The crystal structure for the N-terminal two domains of icam-1
1D3L 3.25 Å, D1D2-icam-1 fully glycosylated, variation of D1-D2 interdomain angle in different…
1MQ8 3.3 Å, Crystal structure of alphaL I domain in complex with ICAM-1
3TCX 3.6 Å, Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain…
6S8U 3.67 Å, Structure of the PfEMP1 IT4var13 DBLbeta domain bound to ICAM-1
6EIT 3.9 Å, Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
1Z7Z 8.0 Å, Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi
1D3I 26.0 Å, cryo-EM structure of human rhinovirus 14 (HRV14) complexed with a two-domain fragment of…

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