Research workbench
Time-resolved crystal structure of hindiii with 60SEC soaking
Analyse Time-resolved crystal structure of hindiii with 60SEC soaking in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WVP
- Type
- protein + DNA
- Length
- 1,336 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme hindiii; DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')…
- EC
- 3.1.21.4
- UniProt
- P43870
- Ligands
- MN
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B | Type-2 restriction enzyme hindiii (EC 3.1.21.4) | protein | 298 | 58% helix, 11% strand | P43870 |
| K, L, I, J, E, F, G, H | DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') | dna | 12 | — | — |
| M, N, Q, R | DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3') | dna | 8 | — | — |
| O, P, S, T | DNA (5'-D(*GP*CP*CP*A)-3') | dna | 4 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains C, F, R, S, D, E, Q, T, A, H, M, P, B, G, N, O
- GOL · Glycerol · additive · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.78 | 0.82 | 72 | empty |
| 2 | 750 | 0.77 | 0.82 | 66 | empty |
| 3 | 188 | 0.73 | 0.90 | 30 | empty |
| 4 | 172 | 0.72 | 0.90 | 31 | empty |
| 5 | 225 | 0.66 | 0.84 | 29 | empty |
Interfaces
78 interfaces between chains.
- A–B · 3498 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 3472 Ų buried · 31 hydrogen bonds · protein-protein
- G–N · 936 Ų buried · 323 hydrogen bonds · nucleic-nucleic
- A–G · 864 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–E · 852 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 3WVP · Time-Resolved Crystal Structure of HindIII with 60sec soaking · the same entry in another collection · chain T against T, 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 P43870
- Elsewhere: RCSB PDB 3WVP · PDBe 3WVP · UniProt P43870
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.