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Crystal form BH1

Analyse Crystal form BH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2R6A
Type: protein
Length: 935 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replicative helicase; Dnag primase, helicase binding domain
EC: 2.7.7.-
UniProt: Q9X4C9, Q9X4D0
Ligands: SO4
Pockets: 11 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Replicative helicase	protein	420	52% helix, 13% strand	Q9X4C9
B	Replicative helicase	protein	374	53% helix, 14% strand	Q9X4C9
C	Dnag primase, helicase binding domain (EC 2.7.7.-)	protein	141	69% helix, 0% strand	Q9X4D0

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

11 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	169	0.67	0.87	21	empty
2	476	0.60	0.74	38	empty
3	328	0.59	0.77	44	empty
4	216	0.52	0.77	26	empty
5	238	0.47	0.73	32	empty

Interfaces

3 interfaces between chains.

A–B · 2221 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 646 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 614 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

2R6A · Crystal Form BH1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9X4D0 · AlphaFold monomer V2.0 prediction for DNA primase (Q9X4D0) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 Q9X4C9
Every structure of UniProt Q9X4D0
Elsewhere: RCSB PDB 2R6A · PDBe 2R6A · UniProt Q9X4C9 · UniProt Q9X4D0

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