MolNFT v1 · #141048 · protein

Crystal structure of ssb protein from pseudomonas aeruginosa PAO1

5YUO · Single-stranded DNA-binding protein: “Crystal structure of ssb protein from pseudomonas aeruginosa PAO1”. X-ray diffraction, 4 pockets (best druggability 0.65). MolNFT v1 #141048 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5YUO
Type: protein
Length: 408 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein
UniProt: P40947
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein	protein	101	9% helix, 59% strand	P40947
B	Single-stranded DNA-binding protein	protein	100	9% helix, 60% strand	P40947
C	Single-stranded DNA-binding protein	protein	105	9% helix, 59% strand	P40947
D	Single-stranded DNA-binding protein	protein	102	9% helix, 61% strand	P40947

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	374	0.65	0.79	55	empty
2	450	0.63	0.77	52	empty
3	188	0.52	0.78	35	empty
4	137	0.51	0.80	27	empty

Interfaces

6 interfaces between chains.

C–D · 1204 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1173 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 373 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 337 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 295 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5YUO · Crystal structure of SSB protein from Pseudomonas aeruginosa PAO1 · the same entry in another collection · chain D against D, TM-score 1.00
P40947 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (P40947) · a predicted model of the same protein · chain D 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 P40947
Elsewhere: RCSB PDB 5YUO · PDBe 5YUO · UniProt P40947

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