MolNFT v1 · #144056 · protein + DNA

B. subtilis ssba with DNA

6BHX · Single-stranded DNA-binding protein a: “B. subtilis ssba with DNA”. X-ray diffraction, 7 pockets (best druggability 0.54). MolNFT v1 #144056 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6BHX
Type: protein + DNA
Length: 406 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein a; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
UniProt: P37455
Pockets: 7 · best druggability 0.54

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein a	protein	98	10% helix, 57% strand	P37455
B	Single-stranded DNA-binding protein a	protein	98	10% helix, 59% strand	P37455
C	Single-stranded DNA-binding protein a	protein	102	10% helix, 59% strand	P37455
D	Single-stranded DNA-binding protein a	protein	97	10% helix, 62% strand	P37455
E	DNA (5'-D(PTPTPTPTPTPTPTPTPTPTP*T)-3')	dna	11	—	—

Pockets

7 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	256	0.54	0.77	40	empty
2	96	0.44	0.80	19	empty
3	79	0.37	0.77	14	empty
4	67	0.32	0.76	14	empty
5	57	0.29	0.75	11	empty

Interfaces

9 interfaces between chains.

B–C · 1357 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1272 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 531 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 513 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 470 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

6BHX · B. subtilis SsbA with DNA · the same entry in another collection · chain E against E, TM-score 1.00
P37455 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein a (P37455) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 P37455
Elsewhere: RCSB PDB 6BHX · PDBe 6BHX · UniProt P37455

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