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Complex structure of proteus mirablis dsba (C30S) with a non- covalently bound peptide pwatcds
Analyse Complex structure of proteus mirablis dsba (C30S) with a non- covalently bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OD7
- Type
- protein
- Length
- 582 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein; (ACE)PWATCDS(NH2) peptide
- UniProt
- B4EZ68
- Ligands
- ACE, SCN, NH2
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | THIOL:DISULFIDE interchange protein | protein | 187 | 50% helix, 12% strand | B4EZ68 |
| D, E, F | (ACE)PWATCDS(NH2) peptide | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains D, E, F
- SCN · Thiocyanate ion · ion · 4 copies · chains A, D, C, E
- NH2 · Amino group · ion · 3 copies · chains A, D, C, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.72 | 0.76 | 88 | empty |
| 2 | 135 | 0.50 | 0.79 | 24 | empty |
| 3 | 94 | 0.45 | 0.79 | 23 | SCN |
| 4 | 120 | 0.38 | 0.74 | 21 | empty |
| 5 | 95 | 0.34 | 0.74 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–F · 497 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 490 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 441 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 225 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4OD7 · Complex structure of Proteus mirablis DsbA (C30S) with a non-covalently bound peptide… · the same entry in another collection · chain A against A, 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 B4EZ68
- Elsewhere: RCSB PDB 4OD7 · PDBe 4OD7 · UniProt B4EZ68
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