MolNFT v1 · #171383 · protein
MEC1-DDC2 (F2244L mutant) in complex with mg AMP-pnp (state II)
6Z2X · DNA damage checkpoint protein LCD1: “MEC1-DDC2 (F2244L mutant) in complex with mg AMP-pnp (state II)”. Electron microscopy, 3 ligands (ANP, MG, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #171383 on GenesisL1: 3D structure…
- PDB
- 6Z2X
- Type
- protein
- Length
- 5,766 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage checkpoint protein LCD1; SERINE/THREONINE-protein kinase MEC1
- EC
- 2.7.11.1
- UniProt
- Q04377, P38111
- Ligands
- ANP, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 56% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | DNA damage checkpoint protein LCD1 | protein | 558 | 56% helix, 2% strand | Q04377 |
| E, F | SERINE/THREONINE-protein kinase MEC1 (EC 2.7.11.1) | protein | 2325 | 56% helix, 2% strand | P38111 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 4 copies · chains E, F
- ZN · Zinc ion · metal · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.87 | 0.88 | 119 | empty |
| 2 | 1147 | 0.85 | 0.86 | 116 | empty |
| 3 | 1133 | 0.82 | 0.83 | 118 | empty |
| 4 | 880 | 0.82 | 0.84 | 85 | empty |
| 5 | 1055 | 0.81 | 0.82 | 96 | empty |
Interfaces
6 interfaces between chains.
- D–E · 7587 Ų buried · 83 hydrogen bonds · protein-protein
- C–F · 7547 Ų buried · 81 hydrogen bonds · protein-protein
- E–F · 2741 Ų buried · 20 hydrogen bonds · protein-protein
- D–C · 1109 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 322 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Z2X · Mec1-Ddc2 (F2244L mutant) in complex with Mg AMP-PNP (State II) · the same entry in another collection · chain D against D, TM-score 1.00
- P38111 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase MEC1 (P38111) · a predicted model of the same protein · chain E against A, TM-score 0.97
- Q04377 · AlphaFold monomer V2.0 prediction for DNA damage checkpoint protein LCD1 (Q04377) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 Q04377
- Every structure of UniProt P38111
- Elsewhere: RCSB PDB 6Z2X · PDBe 6Z2X · UniProt Q04377 · UniProt P38111
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