MolNFT v1 · #129212 · protein + DNA

Salinibacter ruber single-strand binding protein

5ODN · Single-stranded DNA-binding protein: “Salinibacter ruber single-strand binding protein”. X-ray diffraction, 17 pockets (best druggability 0.84). MolNFT v1 #129212 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ODN
Type: protein + DNA
Length: 853 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein; DNA (5'-D(P*TP*TP*TP*T)-3')
UniProt: Q2S565
Pockets: 17 · best druggability 0.84

Structure

x-ray diffraction · 9 distinct chains · 10% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	Single-stranded DNA-binding protein	protein	99	10% helix, 62% strand	Q2S565
B	Single-stranded DNA-binding protein	protein	106	9% helix, 63% strand	Q2S565
C	Single-stranded DNA-binding protein	protein	102	10% helix, 61% strand	Q2S565
D	Single-stranded DNA-binding protein	protein	106	9% helix, 59% strand	Q2S565
E	Single-stranded DNA-binding protein	protein	105	10% helix, 64% strand	Q2S565
F	Single-stranded DNA-binding protein	protein	105	10% helix, 64% strand	Q2S565
G	Single-stranded DNA-binding protein	protein	102	10% helix, 64% strand	Q2S565
I, M, J, K, Q	DNA (5'-D(PTPTPTPT)-3')	dna	4	—	—
N, P, L	DNA (5'-D(PTPTPTPT)-3')	dna	3	—	—

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	817	0.84	0.87	115	empty
2	102	0.58	0.86	20	empty
3	63	0.57	0.89	27	empty
4	107	0.54	0.83	23	empty
5	218	0.54	0.78	42	empty

Interfaces

35 interfaces between chains.

D–F · 1122 Å² buried · 21 hydrogen bonds · protein-protein
E–H · 1119 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1072 Å² buried · 19 hydrogen bonds · protein-protein
A–G · 1051 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1029 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5ODN · Salinibacter ruber Single-Strand Binding protein · the same entry in another collection · chain A against A, 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 Q2S565
Elsewhere: RCSB PDB 5ODN · PDBe 5ODN · UniProt Q2S565

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