Research workbench
Twelve chloride ions drive assembly of human ALPHA345 collagen IV NC1 domain
Analyse Twelve chloride ions drive assembly of human ALPHA345 collagen IV NC1 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WKU
- Type
- protein
- Length
- 677 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-3(IV) CHAIN,COLLAGEN alpha-4(IV) chain, collagen alpha-5(IV) chain
- UniProt
- Q01955, P53420, P29400
- Ligands
- CL
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen alpha-3(IV) CHAIN,COLLAGEN alpha-4(IV) chain, collagen alpha-5(IV) chain | protein | 677 | 11% helix, 43% strand | Q01955, P53420, P29400 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A
- EDO · 1,2-ethanediol · additive · 30 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 24 copies · chains A
- PGE · Triethylene glycol · additive · 20 copies · chains A
- PG4 · Tetraethylene glycol · additive · 10 copies · chains A
- P6G · Hexaethylene glycol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.86 | 0.87 | 82 | PGE, PEG, EDO |
| 2 | 98 | 0.64 | 0.89 | 20 | P6G |
| 3 | 113 | 0.53 | 0.83 | 26 | EDO |
| 4 | 102 | 0.48 | 0.80 | 22 | EDO, PEG |
| 5 | 104 | 0.46 | 0.79 | 20 | PGE |
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 6WKU · Twelve Chloride Ions Drive Assembly of Human alpha345 Collagen IV NC1 domain · the same entry in another collection · chain A against A, TM-score 1.00
- P29400 · AlphaFold monomer V2.0 prediction for collagen alpha-5(IV) chain (P29400) · a predicted model of the same protein · chain A against A, TM-score 0.38
- Q01955 · AlphaFold monomer V2.0 prediction for collagen alpha-3(IV) chain (Q01955) · a predicted model of the same protein · chain A against A, TM-score 0.38
- P53420 · AlphaFold monomer V2.0 prediction for collagen alpha-4(IV) chain (P53420) · a predicted model of the same protein · chain A against A, TM-score 0.37
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 Q01955
- Every structure of UniProt P53420
- Every structure of UniProt P29400
- Elsewhere: RCSB PDB 6WKU · PDBe 6WKU · UniProt Q01955 · UniProt P53420 · UniProt P29400
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