Research workbench
Connectase MJ0548 from methanocaldococcus jannaschii in complex with an mtra-derived peptide
Analyse Connectase MJ0548 from methanocaldococcus jannaschii in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZW0
- Type
- protein
- Length
- 650 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Connectase MJ0548; Tetrahydromethanopterin S-methyltransferase subunit a
- EC
- 2.1.1.86
- UniProt
- Q57968, Q58261
- Ligands
- QRE
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Connectase MJ0548 | protein | 299 | 29% helix, 36% strand | Q57968 |
| C, D | Tetrahydromethanopterin S-methyltransferase subunit a (EC 2.1.1.86) | protein | 26 | 31% helix, 27% strand | Q58261 |
Ligands and binding sites
- QRE · 2-[3,6-bis(oxidanyl)-9~{H}-xanthen-9-yl]-5-[(6-oxidanyl-6-oxidanylidene-hexyl) carbamothioylamino]benzoic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.77 | 0.85 | 38 | empty |
| 2 | 467 | 0.76 | 0.85 | 38 | empty |
| 3 | 212 | 0.65 | 0.83 | 31 | QRE |
| 4 | 222 | 0.65 | 0.83 | 27 | QRE |
| 5 | 154 | 0.55 | 0.81 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1617 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1481 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1472 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 222 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 206 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ZW0 · Connectase MJ0548 from Methanocaldococcus jannaschii in complex with an MtrA-derived… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57968 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ0548 (Q57968) · a predicted model of the same protein · chain A against A, TM-score 0.89
- Q58261 · AlphaFold monomer V2.0 prediction for tetrahydromethanopterin S-methyltransferase subunit… · a predicted model of the same protein · chain C against A, TM-score 0.32
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 Q57968
- Every structure of UniProt Q58261
- Elsewhere: RCSB PDB 6ZW0 · PDBe 6ZW0 · UniProt Q57968 · UniProt Q58261
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