3TCX: Intercellular adhesion molecule 1
Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation. Determined by X-ray diffraction at 3.6 Å resolution. Released 31 Aug 2011.
- Method
- X-ray diffraction
- Resolution
- 3.6 Å
- Organism
- Homo sapiens
- Chains
- 28
- Atoms
- 29,330
- Mol. weight
- 418.06 kDa
- Ligands
- MG
- Released
- 31 Aug 2011
Explore 3TCX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3TCX contains 124 α-helices and 196 β-strands across 28 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.
Chains a, A, C, E, G, I, K, M, O, Q, S, U, W and Y: 0 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-5 | 4 | 3 |
| β-strand | 8-12 | 5 | 4 |
| β-strand | 15-23 | 9 | 3 |
| β-strand | 30-34 | 5 | 4 |
| β-strand | 39-41 | 3 | 3 |
| β-strand | 49-57 | 9 | 3 |
| β-strand | 61-68 | 8 | 4 |
| β-strand | 73-83 | 11 | 4 |
Chains b, B, F, H, J and N: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 130-137 | 8 | 6 |
| α-helix | 144-159 | 16 | |
| β-strand | 166-173 | 8 | 6 |
| β-strand | 177-181 | 5 | 6 |
| α-helix | 183-188 | 6 | |
| α-helix | 192-195 | 4 | |
| α-helix | 208-214 | 7 | |
| α-helix | 215-219 | 5 | |
| β-strand | 231-238 | 8 | 6 |
| α-helix | 249-251 | 3 | |
| β-strand | 255-260 | 6 | 6 |
| α-helix | 263-265 | 3 | |
| α-helix | 268-277 | 10 | |
| β-strand | 286-288 | 3 | 6 |
| α-helix | 297-302 | 6 | |
Chains D and V: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 130-137 | 8 | 9 |
| α-helix | 144-159 | 16 | |
| β-strand | 166-173 | 8 | 9 |
| β-strand | 177-181 | 5 | 9 |
| α-helix | 183-188 | 6 | |
| α-helix | 192-195 | 4 | |
| α-helix | 208-214 | 7 | |
| α-helix | 215-219 | 5 | |
| β-strand | 231-238 | 8 | 9 |
| α-helix | 249-251 | 3 | |
| β-strand | 255-260 | 6 | 9 |
| α-helix | 268-277 | 10 | |
| β-strand | 286-288 | 3 | 9 |
| α-helix | 297-302 | 6 | |
Chains L, P, R, X and Z: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 130-137 | 8 | 21 |
| α-helix | 144-159 | 16 | |
| β-strand | 166-173 | 8 | 21 |
| β-strand | 177-181 | 5 | 21 |
| α-helix | 183-188 | 6 | |
| α-helix | 192-195 | 4 | |
| α-helix | 208-214 | 7 | |
| α-helix | 215-219 | 5 | |
| β-strand | 231-238 | 8 | 21 |
| α-helix | 249-251 | 3 | |
| β-strand | 255-260 | 6 | 21 |
| α-helix | 263-265 | 3 | |
| α-helix | 268-277 | 10 | |
| β-strand | 286-288 | 3 | 21 |
| α-helix | 297-305 | 9 | |
Chain T: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 130-137 | 8 | 33 |
| α-helix | 144-159 | 16 | |
| β-strand | 166-173 | 8 | 33 |
| β-strand | 177-181 | 5 | 33 |
| α-helix | 183-189 | 7 | |
| α-helix | 192-195 | 4 | |
| α-helix | 208-214 | 7 | |
| α-helix | 215-219 | 5 | |
| β-strand | 231-238 | 8 | 33 |
| α-helix | 249-251 | 3 | |
| β-strand | 255-260 | 6 | 33 |
| α-helix | 263-265 | 3 | |
| α-helix | 268-277 | 10 | |
| β-strand | 286-288 | 3 | 33 |
| α-helix | 297-305 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Intercellular adhesion molecule 1 | A, C, E, G, I, K, M, O, Q, S, U, W, Y, a | protein | 85 | Homo sapiens | P05362 (AlphaFold model) |
| Integrin alpha-L | B, D, F, H, J, L, N, P, R, T, V, X, Z, b | protein | 180 | Homo sapiens | P20701 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K, M, O, Q, S, U, W, Y, a), FASTA
>3TCX_1 Intercellular adhesion molecule 1 (chains A, C, E, G, I, K, M, O, Q, S, U, W, Y, a)
MVSVSPSKVTLPRGGSVLVTCSASCDQPKLLGIETPLVKKELLLPGNNRKVYELSNVQED
SQVMCYANCPDGQSTAKAFLTVYWT
Sequence of entity 2 (B, D, F, H, J, L, N, P, R, T, V, X, Z, b), FASTA
>3TCX_2 Integrin alpha-L (chains B, D, F, H, J, L, N, P, R, T, V, X, Z, b)
MNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYV
KWKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGN
IDAAKDIIRYIIGIGKHSQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKIY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 14 |
Primary citation
Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity L Integrin I Domain of Native C-Terminal Helix Conformation. Kang, S., Kim, C.U., Gu, X. et al. To be published.
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
- 1P53 3.06 Å, The Crystal Structure of ICAM-1 D3-D5 fragment
- 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
- 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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