Research workbench
MEC1-DDC2 (wild-type) in complex with AMP-pnp
Analyse MEC1-DDC2 (wild-type) in complex with AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z3A
- Type
- protein
- Length
- 5,730 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase MEC1; DNA damage checkpoint protein LCD1
- EC
- 2.7.11.1
- UniProt
- P38111, Q04377
- Ligands
- ANP, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 59% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, E | SERINE/THREONINE-protein kinase MEC1 (EC 2.7.11.1) | protein | 2311 | 59% helix, 2% strand | P38111 |
| C, D | DNA damage checkpoint protein LCD1 | protein | 554 | 58% helix, 2% strand | Q04377 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains F, E
- ZN · Zinc ion · metal · 2 copies · chains F, E
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 | 1103 | 0.87 | 0.89 | 116 | empty |
| 2 | 1171 | 0.86 | 0.87 | 115 | empty |
| 3 | 1104 | 0.84 | 0.85 | 120 | empty |
| 4 | 957 | 0.82 | 0.84 | 103 | empty |
| 5 | 511 | 0.80 | 0.87 | 63 | empty |
Interfaces
6 interfaces between chains.
- F–D · 7595 Ų buried · 89 hydrogen bonds · protein-protein
- C–E · 7594 Ų buried · 93 hydrogen bonds · protein-protein
- F–E · 2405 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 6 hydrogen bonds · protein-protein
- F–C · 324 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Z3A · Mec1-Ddc2 (wild-type) in complex with AMP-PNP · the same entry in another collection · chain F against F, 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 F against A, TM-score 0.95
- Q04377 · AlphaFold monomer V2.0 prediction for DNA damage checkpoint protein LCD1 (Q04377) · a predicted model of the same protein · chain C 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 P38111
- Every structure of UniProt Q04377
- Elsewhere: RCSB PDB 6Z3A · PDBe 6Z3A · UniProt P38111 · UniProt Q04377
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