Research workbench
Crystal structures of homooligomers of collagen type IV. ALPHA1NC1
Analyse Crystal structures of homooligomers of collagen type IV. ALPHA1NC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NAY
- Type
- protein
- Length
- 1,370 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-1(IV) chain
- UniProt
- P02462
- Ligands
- CL, SO4
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Collagen alpha-1(IV) chain | protein | 228 | 10% helix, 43% strand | P02462 |
| E, F | Collagen alpha-1(IV) chain | protein | 229 | 10% helix, 43% strand | P02462 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, D, C, F, B, E
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.89 | 0.91 | 112 | empty |
| 2 | 1077 | 0.86 | 0.87 | 76 | empty |
| 3 | 86 | 0.49 | 0.82 | 20 | empty |
| 4 | 125 | 0.48 | 0.79 | 25 | CL |
| 5 | 86 | 0.48 | 0.82 | 22 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2405 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 2402 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2401 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2394 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2387 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 5NAY · Crystal structures of homooligomers of collagen type IV. alpha1NC1 · 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 D against A, 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 P02462
- Elsewhere: RCSB PDB 5NAY · PDBe 5NAY · UniProt P02462
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