MolNFT v1 · #14253 · protein
Structure of type IV collagen NC1 domains
1M3D · Type IV collagen noncollagenous domain- ALPHA1: “Structure of type IV collagen NC1 domains”. X-ray diffraction, 2 ligands (LU, BR), 20 pockets (best druggability 0.88). MolNFT v1 #14253 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1M3D
- Type
- protein
- Length
- 2,681 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV collagen noncollagenous domain- ALPHA1; Type IV collagen noncollagenous domain…
- UniProt
- Q7SIB2, Q7SIB3
- Ligands
- LU, BR
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Type IV collagen noncollagenous domain- ALPHA1 | protein | 223 | 10% helix, 44% strand | Q7SIB2 |
| B, K | Type IV collagen noncollagenous domain- ALPHA1 | protein | 224 | 10% helix, 43% strand | Q7SIB2 |
| C, I, L | Type IV collagen noncollagenous domain- ALPHA2 | protein | 222 | 9% helix, 45% strand | Q7SIB3 |
| D, G | Type IV collagen noncollagenous domain- ALPHA1 | protein | 225 | 10% helix, 44% strand | Q7SIB2 |
| E, H | Type IV collagen noncollagenous domain- ALPHA1 | protein | 224 | 10% helix, 44% strand | Q7SIB2 |
| F | Type IV collagen noncollagenous domain- ALPHA2 | protein | 223 | 9% helix, 45% strand | Q7SIB3 |
Ligands and binding sites
- LU · Lutetium (III) ion · metal · 4 copies · chains C, E, F, B, I, K, L
- BR · Bromide ion · ion · 36 copies · chains A, B, D, E, F, C, H, G, J, K, I, L
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
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 | 931 | 0.88 | 0.90 | 105 | LU |
| 2 | 444 | 0.86 | 0.93 | 66 | LU |
| 3 | 729 | 0.85 | 0.89 | 81 | empty |
| 4 | 984 | 0.83 | 0.84 | 91 | BR, GOL |
| 5 | 176 | 0.75 | 0.91 | 38 | empty |
Interfaces
28 interfaces between chains.
- E–F · 2262 Ų buried · 39 hydrogen bonds · protein-protein
- H–I · 2261 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2241 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2200 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2199 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide (disulfide).
Compared structures
- 1M3D · Structure of Type IV Collagen NC1 Domains · the same entry in another collection · chain L against L, 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 Q7SIB2
- Every structure of UniProt Q7SIB3
- Elsewhere: RCSB PDB 1M3D · PDBe 1M3D · UniProt Q7SIB2 · UniProt Q7SIB3
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