Research workbench
Crystal structure of type IV collagen NC1 domain from bovine lens capsule
Analyse Crystal structure of type IV collagen NC1 domain from bovine lens capsule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T60
- Type
- protein
- Length
- 5,381 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV collagen
- Ligands
- K, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 13 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Type IV collagen | protein | 223 | 10% helix, 42% strand | — |
| B, P, S | Type IV collagen | protein | 225 | 8% helix, 44% strand | — |
| C | Type IV collagen | protein | 223 | 7% helix, 45% strand | — |
| D, J, K, Q, V, W | Type IV collagen | protein | 224 | 10% helix, 44% strand | — |
| E | Type IV collagen | protein | 224 | 10% helix, 44% strand | — |
| F | Type IV collagen | protein | 222 | 9% helix, 45% strand | — |
| G | Type IV collagen | protein | 228 | 10% helix, 44% strand | — |
| H, T | Type IV collagen | protein | 227 | 8% helix, 43% strand | — |
| I | Type IV collagen | protein | 225 | 7% helix, 44% strand | — |
| L | Type IV collagen | protein | 221 | 9% helix, 44% strand | — |
| N | Type IV collagen | protein | 224 | 10% helix, 43% strand | — |
| O, R, U | Type IV collagen | protein | 224 | 9% helix, 44% strand | — |
| X | Type IV collagen | protein | 223 | 7% helix, 45% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 16 copies · chains B, C, F, A, E, D, G, I, K, H, L, J, M, O, Q, N, R, P, T, U, X, S, W, V
- CL · Chloride ion · ion · 16 copies · chains A, C, D, F, G, J, I, H, L, M, O, P, R, S, V, U, X
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A, C, D, F, G, J, L, M, O, P, R, S, U, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.89 | 0.91 | 115 | empty |
| 2 | 1029 | 0.89 | 0.90 | 114 | empty |
| 3 | 816 | 0.87 | 0.89 | 75 | empty |
| 4 | 1114 | 0.87 | 0.88 | 82 | empty |
| 5 | 1106 | 0.86 | 0.87 | 82 | empty |
Interfaces
62 interfaces between chains.
- S–T · 2304 Ų buried · 36 hydrogen bonds · protein-protein
- Q–R · 2302 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 2301 Ų buried · 33 hydrogen bonds · protein-protein
- T–U · 2298 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2295 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 144 disulfide (disulfide).
Compared structures
- 1T60 · Crystal structure of Type IV collagen NC1 domain from bovine lens capsule · the same entry in another collection · 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
- Elsewhere: RCSB PDB 1T60 · PDBe 1T60
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.