MolNFT v1 · #12219 · protein

Crystal structure of the phage P4 origin-binding domain

1KA8 · Putative P4-specific DNA primase: “Crystal structure of the phage P4 origin-binding domain”. X-ray diffraction, 2 pockets (best druggability 0.57). MolNFT v1 #12219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KA8
Type: protein
Length: 600 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative P4-specific DNA primase
EC: 2.7.7.-
UniProt: P10277
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Putative P4-specific DNA primase (EC 2.7.7.-)	protein	100	38% helix, 16% strand	P10277

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	205	0.57	0.79	31	empty
2	51	0.23	0.72	13	empty

Interfaces

5 interfaces between chains.

B–D · 673 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 671 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 658 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 626 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 229 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1KA8 · Crystal Structure of the Phage P4 Origin-Binding Domain · 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 P10277
Elsewhere: RCSB PDB 1KA8 · PDBe 1KA8 · UniProt P10277

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