MolNFT v1 · #22463 · protein
Crystal structure of type IV collagen NC1 domain from bovine lens capsule
1T60: “Crystal structure of type IV collagen NC1 domain from bovine lens capsule”. X-ray diffraction, 2 ligands (K, CL), 20 pockets (best druggability 0.89). MolNFT v1 #22463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
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