MolNFT v1 · #54842 · protein
Structure of MECA121 & clpc N-domain complex
2Y1R · Negative regulator of genetic competence CLPC/MECB: “Structure of MECA121 & clpc N-domain complex”. X-ray diffraction, 1 ligand (SRT), 20 pockets (best druggability 0.59). MolNFT v1 #54842 on GenesisL1: 3D structure, binding sites…
- PDB
- 2Y1R
- Type
- protein
- Length
- 1,756 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Negative regulator of genetic competence CLPC/MECB; Adapter protein meca 1
- UniProt
- P37571, P37958
- Ligands
- SRT
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 11 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Negative regulator of genetic competence CLPC/MECB | protein | 140 | 66% helix, 4% strand | P37571 |
| B, C, E, G, H | Negative regulator of genetic competence CLPC/MECB | protein | 139 | 67% helix, 4% strand | P37571 |
| D | Negative regulator of genetic competence CLPC/MECB | protein | 141 | 66% helix, 4% strand | P37571 |
| F | Negative regulator of genetic competence CLPC/MECB | protein | 133 | 69% helix, 5% strand | P37571 |
| I, P | Adapter protein meca 1 | protein | 94 | 38% helix, 29% strand | P37958 |
| J | Adapter protein meca 1 | protein | 95 | 38% helix, 28% strand | P37958 |
| K | Adapter protein meca 1 | protein | 92 | 39% helix, 29% strand | P37958 |
| L | Adapter protein meca 1 | protein | 4 | 0% helix, 0% strand | P37958 |
| M | Adapter protein meca 1 | protein | 90 | 40% helix, 30% strand | P37958 |
| N | Adapter protein meca 1 | protein | 89 | 40% helix, 30% strand | P37958 |
| O | Adapter protein meca 1 | protein | 89 | 40% helix, 30% strand | P37958 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 16 copies · chains A, B, K, C, J, D, I, E, P, F, O, G, N, H, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.59 | 0.79 | 34 | empty |
| 2 | 238 | 0.57 | 0.79 | 34 | empty |
| 3 | 357 | 0.57 | 0.76 | 48 | empty |
| 4 | 240 | 0.56 | 0.78 | 33 | empty |
| 5 | 257 | 0.55 | 0.77 | 33 | empty |
Interfaces
33 interfaces between chains.
- B–J · 665 Ų buried · 15 hydrogen bonds · protein-protein
- G–O · 661 Ų buried · 17 hydrogen bonds · protein-protein
- F–N · 652 Ų buried · 16 hydrogen bonds · protein-protein
- A–I · 650 Ų buried · 15 hydrogen bonds · protein-protein
- E–M · 648 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2Y1R · Structure of MecA121 & ClpC N-domain complex · the same entry in another collection · chain K against K, 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 P37571
- Every structure of UniProt P37958
- Elsewhere: RCSB PDB 2Y1R · PDBe 2Y1R · UniProt P37571 · UniProt P37958
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