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Crystal structure of collagen IV NC1 domain from placenta basement membrane
Analyse Crystal structure of collagen IV NC1 domain from placenta basement membrane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T61
- Type
- protein
- Length
- 1,338 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV collagen
- UniProt
- Q7SIB3
- Ligands
- K, CA, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type IV collagen | protein | 223 | 10% helix, 44% strand | — |
| B | Type IV collagen | protein | 223 | 10% helix, 45% strand | — |
| C, F | Type IV collagen | protein | 222 | 9% helix, 45% strand | Q7SIB3 |
| D, E | Type IV collagen | protein | 224 | 10% helix, 44% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, D, E, B, C, F
- CA · Calcium ion · metal · 2 copies · chains C, E, F, B
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.88 | 0.91 | 95 | CA |
| 2 | 609 | 0.81 | 0.86 | 51 | empty |
| 3 | 321 | 0.78 | 0.88 | 51 | empty |
| 4 | 58 | 0.61 | 0.92 | 20 | empty |
| 5 | 107 | 0.61 | 0.87 | 25 | GOL |
Interfaces
13 interfaces between chains.
- E–F · 2244 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2203 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2182 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 2162 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2136 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 1T61 · crystal structure of collagen IV NC1 domain from placenta basement membrane · the same entry in another collection · chain F against F, TM-score 1.00
- Q7SIB3 · AlphaFold monomer V2.0 prediction for collagen alpha-2(IV) chain (Q7SIB3) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 Q7SIB3
- Elsewhere: RCSB PDB 1T61 · PDBe 1T61 · UniProt Q7SIB3
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