Research workbench
Protein-protein complex of subunit 1 and 2 of molybdopterin-converting factor from helicobacter pylori 26695
Analyse Protein-protein complex of subunit 1 and 2 of molybdopterin-converting factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RPF
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdopterin synthase catalytic subunit; Molybdopterin converting factor, subunit 1…
- EC
- 2.-.-.-
- UniProt
- P56422, O25482
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Molybdopterin synthase catalytic subunit (EC 2.-.-.-) | protein | 145 | 36% helix, 37% strand | P56422 |
| B | Molybdopterin synthase catalytic subunit (EC 2.-.-.-) | protein | 146 | 34% helix, 37% strand | P56422 |
| C | Molybdopterin converting factor, subunit 1 (moad) | protein | 74 | 12% helix, 30% strand | O25482 |
| D | Molybdopterin converting factor, subunit 1 (moad) | protein | 63 | 11% helix, 27% strand | O25482 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.36 | 0.75 | 19 | empty |
| 2 | 91 | 0.34 | 0.74 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1317 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1182 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 248 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 76 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3RPF · Protein-protein complex of subunit 1 and 2 of Molybdopterin-converting factor from… · the same entry in another collection · chain A against A, TM-score 1.00
- P56422 · AlphaFold monomer V2.0 prediction for molybdopterin synthase catalytic subunit (P56422) · 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 P56422
- Every structure of UniProt O25482
- Elsewhere: RCSB PDB 3RPF · PDBe 3RPF · UniProt P56422 · UniProt O25482
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