Research workbench
Crystal structures of homooligomers of the non-collagenous domains of collagen type IV. ALPHA121NC1
Analyse Crystal structures of homooligomers of the non-collagenous domains of collagen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NAX
- Type
- protein
- Length
- 1,348 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-1(IV) chain; Collagen alpha-2(IV) chain
- UniProt
- P02462, P08572
- Ligands
- CL
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen alpha-1(IV) chain | protein | 226 | 8% helix, 42% strand | P02462 |
| B | Collagen alpha-1(IV) chain | protein | 227 | 8% helix, 44% strand | P02462 |
| C | Collagen alpha-2(IV) chain | protein | 224 | 5% helix, 43% strand | P08572 |
| D | Collagen alpha-1(IV) chain | protein | 225 | 7% helix, 44% strand | P02462 |
| E | Collagen alpha-2(IV) chain | protein | 223 | 4% helix, 43% strand | P08572 |
| F | Collagen alpha-1(IV) chain | protein | 223 | 10% helix, 43% strand | P02462 |
Ligands and binding sites
- CL · Chloride ion · ion · 11 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.89 | 0.90 | 114 | empty |
| 2 | 1131 | 0.87 | 0.88 | 77 | empty |
| 3 | 100 | 0.56 | 0.85 | 24 | CL |
| 4 | 126 | 0.54 | 0.82 | 23 | CL |
| 5 | 96 | 0.47 | 0.81 | 22 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2430 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2354 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2313 Ų buried · 40 hydrogen bonds · protein-protein
- D–F · 2283 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2252 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 5NAX · Crystal structures of homooligomers of the non-collagenous domains of collagen type IV.… · the same entry in another collection · chain F against F, 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 F against A, TM-score 1.00
- P08572 · AlphaFold monomer V2.0 prediction for collagen alpha-2(IV) chain (P08572) · a predicted model of the same protein · chain C 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 P02462
- Every structure of UniProt P08572
- Elsewhere: RCSB PDB 5NAX · PDBe 5NAX · UniProt P02462 · UniProt P08572
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