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Time-resolved crystal structure of hindiii with 230SEC soaking
Analyse Time-resolved crystal structure of hindiii with 230SEC soaking in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WVK
- Type
- protein + DNA
- Length
- 1,288 residues
- Chains
- 16
- 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
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Type-2 restriction enzyme hindiii (EC 3.1.21.4) | protein | 298 | 59% helix, 11% strand | P43870 |
| M, N, O, P | DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') | dna | 12 | — | — |
| E, G, I, K | DNA (5'-D(*GP*CP*CP*A)-3') | dna | 4 | — | — |
| F, H, J, L | DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, F, E, B, H, G, C, J, I, D, L, K
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
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 | 928 | 0.79 | 0.82 | 60 | empty |
| 2 | 921 | 0.79 | 0.82 | 62 | empty |
| 3 | 326 | 0.70 | 0.84 | 36 | empty |
| 4 | 193 | 0.70 | 0.88 | 34 | empty |
| 5 | 171 | 0.70 | 0.89 | 33 | empty |
Interfaces
44 interfaces between chains.
- C–D · 3518 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3459 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 659 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 644 Ų buried · 10 hydrogen bonds · protein-protein
- D–L · 623 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 3WVK · Time-Resolved Crystal Structure of HindIII with 230sec soaking · 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 P43870
- Elsewhere: RCSB PDB 3WVK · PDBe 3WVK · UniProt P43870
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