MolNFT v1 · #127923 · protein
Crystal structures of homooligomers of collagen type IV. ALPHA3NC1
5NB0 · Collagen alpha-3(IV) chain: “Crystal structures of homooligomers of collagen type IV. ALPHA3NC1”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.86). MolNFT v1 #127923 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NB0
- Type
- protein
- Length
- 1,804 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-3(IV) chain
- UniProt
- Q01955
- Ligands
- CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, H | Collagen alpha-3(IV) chain | protein | 225 | 8% helix, 43% strand | Q01955 |
| B, F | Collagen alpha-3(IV) chain | protein | 226 | 7% helix, 42% strand | Q01955 |
| D | Collagen alpha-3(IV) chain | protein | 227 | 7% helix, 42% strand | Q01955 |
Ligands and binding sites
- CL · Chloride ion · ion · 16 copies · chains A, D, F, B, E, C, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.86 | 0.87 | 75 | empty |
| 2 | 1108 | 0.86 | 0.87 | 76 | empty |
| 3 | 277 | 0.85 | 0.97 | 34 | empty |
| 4 | 670 | 0.70 | 0.77 | 75 | empty |
| 5 | 796 | 0.66 | 0.74 | 74 | CL |
Interfaces
20 interfaces between chains.
- D–F · 2277 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2272 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2265 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2236 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2199 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 5NB0 · Crystal structures of homooligomers of collagen type IV. alpha3NC1 · the same entry in another collection · chain H against H, TM-score 1.00
- 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 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 Q01955
- Elsewhere: RCSB PDB 5NB0 · PDBe 5NB0 · UniProt Q01955
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