MolNFT v1 · #118129 · protein + DNA
Crystal structure of laglidadg meganuclease I-panmi with coordinated calcium ions
5ESP: “Crystal structure of laglidadg meganuclease I-panmi with coordinated calcium ions”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.68). MolNFT v1 #118129 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ESP
- Type
- protein + DNA
- Length
- 687 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-panmi; DNA (27-mer)
- UniProt
- P15563
- Ligands
- CA
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-panmi | protein | 292 | 48% helix, 21% strand | P15563 |
| B | I-panmi | protein | 288 | 49% helix, 19% strand | P15563 |
| G | DNA (27-mer) | dna | 27 | — | — |
| H, D | DNA (27-mer) | dna | 27 | — | — |
| C | DNA (27-mer) | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, G, H, B, C, D
- GOL · Glycerol · additive · 2 copies · chains G, H, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.68 | 0.81 | 51 | empty |
| 2 | 122 | 0.64 | 0.88 | 24 | empty |
| 3 | 175 | 0.64 | 0.85 | 25 | empty |
| 4 | 217 | 0.62 | 0.82 | 32 | empty |
| 5 | 165 | 0.59 | 0.82 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–H · 1573 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–G · 1531 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–D · 1473 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–C · 1429 Ų buried · 22 hydrogen bonds · protein-nucleic
- G–H · 1270 Ų buried · 104 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ESP · Crystal Structure of LAGLIDADG Meganuclease I-PanMI with coordinated Calcium ions · the same entry in another collection · chain D against D, TM-score 1.00
- P15563 · AlphaFold monomer V2.0 prediction for uncharacterized 49.1 kda protein in ND3 intron… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P15563
- Elsewhere: RCSB PDB 5ESP · PDBe 5ESP · UniProt P15563
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