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Crystal structure of apethermo-dbp-RP2 bound to ssdna DT10

Analyse Crystal structure of apethermo-dbp-RP2 bound to ssdna DT10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PSO
Type: protein + DNA
Length: 1,779 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ssdna binding protein; Polydeoxyribonucleotide
UniProt: Q9YAS7
Ligands: PO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 9 distinct chains · 42% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ssdna binding protein	protein	218	43% helix, 33% strand	Q9YAS7
B, C, H	Ssdna binding protein	protein	220	42% helix, 33% strand	Q9YAS7
D	Ssdna binding protein	protein	219	43% helix, 32% strand	Q9YAS7
F	Ssdna binding protein	protein	219	43% helix, 33% strand	Q9YAS7
G	Ssdna binding protein	protein	217	40% helix, 34% strand	Q9YAS7
I	Ssdna binding protein	protein	221	42% helix, 33% strand	Q9YAS7
L	Polydeoxyribonucleotide	dna	10	—	—
E	Polydeoxyribonucleotide	dna	7	—	—
X, Z	Polydeoxyribonucleotide	dna	4	—	—

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A, B, L

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.88	0.90	115	PO4
2	590	0.82	0.87	64	empty
3	890	0.82	0.83	85	empty
4	225	0.80	0.93	41	empty
5	280	0.79	0.90	39	empty

Interfaces

33 interfaces between chains.

A–D · 2858 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 2850 Å² buried · 30 hydrogen bonds · protein-protein
F–I · 2788 Å² buried · 40 hydrogen bonds · protein-protein
G–H · 2780 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 1004 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4PSO · Crystal structure of apeThermo-DBP-RP2 bound to ssDNA dT10 · 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 Q9YAS7
Elsewhere: RCSB PDB 4PSO · PDBe 4PSO · UniProt Q9YAS7

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