Research workbench
Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV assembled from transition state trimers
Analyse Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MPX
- Type
- protein
- Length
- 673 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein of non-collagenous domains of collagen type IV
- UniProt
- P02462, P08572
- Ligands
- SO4, CL
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion protein of non-collagenous domains of collagen type IV | protein | 673 | 10% helix, 45% strand | P02462, P08572 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A
- CL · Chloride ion · ion · 6 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PGE · Triethylene glycol · additive · chains A
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.86 | 0.87 | 85 | empty |
| 2 | 123 | 0.51 | 0.80 | 22 | GOL |
| 3 | 77 | 0.51 | 0.84 | 23 | empty |
| 4 | 64 | 0.32 | 0.76 | 12 | empty |
| 5 | 71 | 0.32 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 6MPX · Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.38
- P08572 · AlphaFold monomer V2.0 prediction for collagen alpha-2(IV) chain (P08572) · a predicted model of the same protein · chain A against A, TM-score 0.38
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 6MPX · PDBe 6MPX · UniProt P02462 · UniProt P08572
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