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E.COLI primase catalytic core

Analyse E.COLI primase catalytic core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EQN
Type: protein
Length: 1,565 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase
EC: 2.7.7.-
UniProt: P0ABS5
Pockets: 18 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase (EC 2.7.7.-)	protein	315	48% helix, 17% strand	P0ABS5
B	DNA primase (EC 2.7.7.-)	protein	313	46% helix, 18% strand	P0ABS5
C	DNA primase (EC 2.7.7.-)	protein	315	44% helix, 16% strand	P0ABS5
D	DNA primase (EC 2.7.7.-)	protein	314	47% helix, 16% strand	P0ABS5
E	DNA primase (EC 2.7.7.-)	protein	308	48% helix, 18% strand	P0ABS5

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1105	0.84	0.85	102	empty
2	1177	0.81	0.82	97	empty
3	688	0.74	0.80	70	empty
4	239	0.56	0.78	42	empty
5	198	0.55	0.79	30	empty

Interfaces

7 interfaces between chains.

A–B · 767 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 546 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 509 Å² buried · 3 hydrogen bonds · protein-protein
C–E · 447 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 447 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 45 modified (engineered).

Compared structures

1EQN · E.COLI primase catalytic core · the same entry in another collection · chain D against D, TM-score 1.00
P0ABS5 · AlphaFold monomer V2.0 prediction for DNA primase (P0ABS5) · a predicted model of the same protein · chain B 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 P0ABS5
Elsewhere: RCSB PDB 1EQN · PDBe 1EQN · UniProt P0ABS5

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