Research workbench
Structure of engineered single domain icam-1 D1 with high-affinity al integrin I domain of native C-terminal helix conformation
Analyse Structure of engineered single domain icam-1 D1 with high-affinity al integrin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TCX
- Type
- protein
- Length
- 3,710 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intercellular adhesion molecule 1; Integrin alpha-L
- UniProt
- P05362, P20701
- Ligands
- MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W, Y, a | Intercellular adhesion molecule 1 | protein | 85 | 0% helix, 64% strand | P05362 |
| B, D, F, H, J, L, N, P, R, T, V, X, Z, b | Integrin alpha-L | protein | 180 | 33% helix, 21% strand | P20701 |
Ligands and binding sites
- MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.80 | 0.81 | 85 | empty |
| 2 | 142 | 0.75 | 0.93 | 24 | empty |
| 3 | 901 | 0.75 | 0.78 | 81 | empty |
| 4 | 785 | 0.73 | 0.78 | 57 | empty |
| 5 | 790 | 0.72 | 0.78 | 69 | empty |
Interfaces
44 interfaces between chains.
- B–D · 630 Ų buried · 10 hydrogen bonds · protein-protein
- Q–R · 625 Ų buried · 12 hydrogen bonds · protein-protein
- Y–Z · 623 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 622 Ų buried · 15 hydrogen bonds · protein-protein
- S–T · 621 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 3TCX · Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain… · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05362
- Every structure of UniProt P20701
- Elsewhere: RCSB PDB 3TCX · PDBe 3TCX · UniProt P05362 · UniProt P20701
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