MolNFT v1 · #157147 · protein
Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV assembled from transition state trimers
6MPX · Fusion protein of non-collagenous domains of collagen type…: “Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV assembled from transition…”. X-ray diffraction, 2 ligands (SO4, CL), 6 pockets (best…
- 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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