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Crystal structure of the DH/PH fragment of murine dbs in complex with the placental isoform of human CDC42

Analyse Crystal structure of the DH/PH fragment of murine dbs in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KZ7
Type: protein
Length: 1,032 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide exchange factor dbs; CDC42 homolog
UniProt: Q64096, P60953
Pockets: 10 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide exchange factor dbs	protein	337	56% helix, 17% strand	Q64096
B	CDC42 homolog	protein	188	36% helix, 21% strand	P60953
C	Guanine nucleotide exchange factor dbs	protein	330	58% helix, 16% strand	Q64096
D	CDC42 homolog	protein	177	37% helix, 22% strand	P60953

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	619	0.69	0.77	55	empty
2	514	0.68	0.78	58	empty
3	280	0.54	0.76	34	empty
4	238	0.52	0.76	33	empty
5	158	0.51	0.79	26	empty

Interfaces

3 interfaces between chains.

C–D · 1701 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1696 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1104 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

1KZ7 · Crystal Structure of the DH/PH Fragment of Murine Dbs in Complex with the Placental… · the same entry in another collection · chain D against D, TM-score 1.00
Q64096 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor dbs (Q64096) · a predicted model of the same protein · chain A against A, TM-score 0.98
P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 Q64096
Every structure of UniProt P60953
Elsewhere: RCSB PDB 1KZ7 · PDBe 1KZ7 · UniProt Q64096 · UniProt P60953

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