MolNFT v1 · #170909 · protein
RNase 3/1 VERSION1
6YMT · RNase 3/1 version 1: “RNase 3/1 VERSION1”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #170909 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YMT
- Type
- protein
- Length
- 1,514 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNase 3/1 version 1
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, F, H, L | RNase 3/1 version 1 | protein | 125 | 22% helix, 33% strand | — |
| J, C, D, E, K | RNase 3/1 version 1 | protein | 126 | 21% helix, 32% strand | — |
| A, I, B | RNase 3/1 version 1 | protein | 128 | 22% helix, 32% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.83 | 0.93 | 36 | empty |
| 2 | 625 | 0.75 | 0.81 | 88 | empty |
| 3 | 770 | 0.74 | 0.79 | 59 | empty |
| 4 | 643 | 0.72 | 0.79 | 60 | empty |
| 5 | 934 | 0.71 | 0.76 | 73 | empty |
Interfaces
22 interfaces between chains.
- I–B · 697 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 504 Ų buried · 5 hydrogen bonds · protein-protein
- C–L · 497 Ų buried · 4 hydrogen bonds · protein-protein
- J–F · 488 Ų buried · 5 hydrogen bonds · protein-protein
- E–A · 468 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 6YMT · RNASE 3/1 version1 · the same entry in another collection · chain G against G, 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 6YMT · PDBe 6YMT
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