MolNFT v1 · #168581 · protein
Twelve chloride ions drive assembly of human ALPHA345 collagen IV NC1 domain
6WKU · Collagen alpha-3(IV) CHAIN,COLLAGEN alpha-4(IV) chain…: “Twelve chloride ions drive assembly of human ALPHA345 collagen IV NC1 domain”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.86). MolNFT v1 #168581 on…
- 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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