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Crystal structure of yedk in complex with ssdna

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

PDB: 6KBS
Type: protein + DNA
Length: 236 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sos response-associated protein; DNA (5'-D(*CP*GP*GP*TP*CP*GP*AP*TP*TP*C)-3')
EC: 3.4.-.-
UniProt: A0A2S5ZH06
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Sos response-associated protein (EC 3.4.-.-)	protein	227	24% helix, 35% strand	A0A2S5ZH06
D	DNA (5'-D(CPGPGPTPCPGPAPTPTPC)-3')	dna	9	—	—

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.37	0.78	14	empty

Interfaces

1 interface between chains.

B–D · 924 Å² buried · 17 hydrogen bonds · protein-nucleic

Compared structures

6KBS · Crystal structure of yedK in complex with ssDNA · the same entry in another collection · chain B against B, 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 A0A2S5ZH06
Elsewhere: RCSB PDB 6KBS · PDBe 6KBS · UniProt A0A2S5ZH06

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