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B. subtilis SSBB/SSDNA

Analyse B. subtilis SSBB/SSDNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VDY
Type: protein + DNA
Length: 222 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein ssbb; 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP…
UniProt: C0SPB6
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein ssbb	protein	101	10% helix, 55% strand	C0SPB6
B	Single-stranded DNA-binding protein ssbb	protein	97	10% helix, 52% strand	C0SPB6
C, E	5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3'	dna	4	—	—
D, G	5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3'	dna	3	—	—
F	5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3'	dna	10	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	660	0.67	0.76	54	empty
2	118	0.42	0.77	19	empty
3	57	0.33	0.77	19	empty

Interfaces

7 interfaces between chains.

A–F · 563 Å² buried · 8 hydrogen bonds · protein-nucleic
B–C · 392 Å² buried · 3 hydrogen bonds · protein-nucleic
A–E · 360 Å² buried · 3 hydrogen bonds · protein-nucleic
B–G · 321 Å² buried · 5 hydrogen bonds · protein-nucleic
A–B · 289 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3VDY · B. subtilis SsbB/ssDNA · the same entry in another collection · chain G against G, TM-score 1.00
C0SPB6 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein B (C0SPB6) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 C0SPB6
Elsewhere: RCSB PDB 3VDY · PDBe 3VDY · UniProt C0SPB6

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