Research workbench
The 1.9-a crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent met-lys cross-link
Analyse The 1.9-a crystal structure of the noncollagenous (NC1) domain of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LI1
- Type
- protein
- Length
- 1,359 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha 1(IV); Collagen alpha 2(IV)
- UniProt
- P02462, P08572
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Collagen alpha 1(IV) | protein | 228 | 10% helix, 44% strand | P02462 |
| B, E | Collagen alpha 1(IV) | protein | 227 | 10% helix, 44% strand | P02462 |
| C | Collagen alpha 2(IV) | protein | 224 | 7% helix, 46% strand | P08572 |
| F | Collagen alpha 2(IV) | protein | 225 | 7% helix, 45% strand | P08572 |
Ligands and binding sites
- ACT · Acetate ion · additive · 9 copies · chains A, B, D, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.89 | 0.90 | 122 | empty |
| 2 | 782 | 0.86 | 0.89 | 75 | empty |
| 3 | 261 | 0.62 | 0.80 | 38 | ACT |
| 4 | 249 | 0.60 | 0.80 | 41 | ACT |
| 5 | 55 | 0.59 | 0.91 | 20 | empty |
Interfaces
15 interfaces between chains.
- D–E · 2381 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2380 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2275 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2264 Ų buried · 41 hydrogen bonds · protein-protein
- D–F · 2257 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 1LI1 · The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen… · the same entry in another collection · chain F against F, TM-score 1.00
- P02462 · AlphaFold monomer V2.0 prediction for collagen alpha-1(IV) chain (P02462) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P08572 · AlphaFold monomer V2.0 prediction for collagen alpha-2(IV) chain (P08572) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P02462
- Every structure of UniProt P08572
- Elsewhere: RCSB PDB 1LI1 · PDBe 1LI1 · UniProt P02462 · UniProt P08572
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