MolNFT v1 · #127924 · protein
Crystal structures of homooligomers of collagen type IV. ALPHA4NC1
5NB1 · Collagen alpha-4(IV) chain: “Crystal structures of homooligomers of collagen type IV. ALPHA4NC1”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #127924 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5NB1
- Type
- protein
- Length
- 1,247 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-4(IV) chain
- UniProt
- P53420
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen alpha-4(IV) chain | protein | 210 | 9% helix, 32% strand | P53420 |
| B, C, D | Collagen alpha-4(IV) chain | protein | 208 | 8% helix, 33% strand | P53420 |
| E | Collagen alpha-4(IV) chain | protein | 206 | 11% helix, 32% strand | P53420 |
| F | Collagen alpha-4(IV) chain | protein | 207 | 8% helix, 33% strand | P53420 |
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 | 1081 | 0.80 | 0.81 | 121 | empty |
| 2 | 261 | 0.65 | 0.82 | 46 | empty |
| 3 | 273 | 0.61 | 0.80 | 35 | empty |
| 4 | 206 | 0.60 | 0.82 | 34 | empty |
| 5 | 301 | 0.58 | 0.78 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1094 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1093 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 1093 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1061 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 713 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 5NB1 · Crystal structures of homooligomers of collagen type IV. alpha4NC1 · the same entry in another collection · chain F against F, TM-score 1.00
- P53420 · AlphaFold monomer V2.0 prediction for collagen alpha-4(IV) chain (P53420) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 P53420
- Elsewhere: RCSB PDB 5NB1 · PDBe 5NB1 · UniProt P53420
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