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Crystal structure of dsbb-Fab complex

Analyse Crystal structure of dsbb-Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZUQ
Type: protein
Length: 1,162 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Disulfide bond formation protein B; Fab fragment light chain; Fab fragment heavy chain
EC: 1.8.5.-
UniProt: P0A6M2
Ligands: UQ1
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 14% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Disulfide bond formation protein B (EC 1.8.5.-)	protein	148	59% helix, 0% strand	P0A6M2
B, E	Fab fragment light chain	protein	218	6% helix, 41% strand	—
C	Fab fragment heavy chain	protein	216	1% helix, 49% strand	—
F	Fab fragment heavy chain	protein	214	4% helix, 48% strand	—

Ligands and binding sites

UQ1 · Ubiquinone-1 · ligand · 2 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	864	0.79	0.81	79	UQ1
2	969	0.78	0.80	78	UQ1
3	838	0.68	0.75	73	empty
4	265	0.56	0.77	40	empty
5	246	0.50	0.74	38	empty

Interfaces

8 interfaces between chains.

E–F · 1873 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1730 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 458 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 423 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 329 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

2ZUQ · Crystal structure of DsbB-Fab complex · the same entry in another collection · chain F against F, TM-score 1.00
P0A6M2 · AlphaFold monomer V2.0 prediction for disulfide bond formation protein B (P0A6M2) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 P0A6M2
Elsewhere: RCSB PDB 2ZUQ · PDBe 2ZUQ · UniProt P0A6M2

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