MolNFT v1 · #112943 · protein + DNA
The crystal structure of I-scei in complex with its target DNA in the presence of mn
5A0M · Intron-encoded endonuclease I-scei: “The crystal structure of I-scei in complex with its target DNA in the presence of mn”. X-ray diffraction, 1 ligand (MN), 10 pockets (best druggability 0.82). MolNFT v1 #112943 on GenesisL1: 3D…
- PDB
- 5A0M
- Type
- protein + DNA
- Length
- 548 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intron-encoded endonuclease I-scei; 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'…
- EC
- 3.1.-.-
- UniProt
- P03882
- Ligands
- MN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intron-encoded endonuclease I-scei (EC 3.1.-.-) | protein | 224 | 38% helix, 19% strand | P03882 |
| B | Intron-encoded endonuclease I-scei (EC 3.1.-.-) | protein | 227 | 41% helix, 20% strand | P03882 |
| C | 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3' | dna | 13 | — | — |
| D, H | 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3' | dna | 15 | — | — |
| E | 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3' | dna | 14 | — | — |
| I, L | 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3' | dna | 9 | — | — |
| J, K | 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3' | dna | 11 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, C, D, K, L, B, H, J, E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.82 | 0.83 | 89 | empty |
| 2 | 69 | 0.57 | 0.89 | 20 | empty |
| 3 | 72 | 0.55 | 0.87 | 19 | empty |
| 4 | 69 | 0.54 | 0.87 | 19 | empty |
| 5 | 93 | 0.53 | 0.85 | 21 | empty |
Interfaces
21 interfaces between chains.
- A–D · 964 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–H · 961 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–E · 745 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 726 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–J · 712 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 5A0M · The crystal structure of I-scei in complex with its target DNA in the presence of mn · the same entry in another collection · chain L against L, TM-score 1.00
- P03882 · AlphaFold monomer V2.0 prediction for intron-encoded endonuclease I-scei (P03882) · a predicted model of the same protein · chain B 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
- Every structure of UniProt P03882
- Elsewhere: RCSB PDB 5A0M · PDBe 5A0M · UniProt P03882
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