MolNFT v1 · #143092 · protein

Crystal structure of the DNA polymerase III subunit beta from acinetobacter baumannii

6AP4: “Crystal structure of the DNA polymerase III subunit beta from acinetobacter baumannii”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.84). MolNFT v1 #143092 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6AP4
Type: protein
Length: 6,002 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase III subunit beta
UniProt: V5V7W3
Ligands: MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 15 distinct chains · 21% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase III subunit beta	protein	378	21% helix, 42% strand	V5V7W3
B, E	DNA polymerase III subunit beta	protein	382	20% helix, 42% strand	V5V7W3
C	DNA polymerase III subunit beta	protein	379	20% helix, 41% strand	V5V7W3
D	DNA polymerase III subunit beta	protein	382	21% helix, 40% strand	V5V7W3
F	DNA polymerase III subunit beta	protein	379	21% helix, 43% strand	V5V7W3
G	DNA polymerase III subunit beta	protein	378	22% helix, 40% strand	V5V7W3
H	DNA polymerase III subunit beta	protein	383	21% helix, 41% strand	V5V7W3
I	DNA polymerase III subunit beta	protein	370	23% helix, 42% strand	V5V7W3
J	DNA polymerase III subunit beta	protein	384	22% helix, 43% strand	V5V7W3
K	DNA polymerase III subunit beta	protein	365	21% helix, 37% strand	V5V7W3
L	DNA polymerase III subunit beta	protein	356	22% helix, 40% strand	V5V7W3
M	DNA polymerase III subunit beta	protein	378	21% helix, 41% strand	V5V7W3
N	DNA polymerase III subunit beta	protein	372	22% helix, 40% strand	V5V7W3
O	DNA polymerase III subunit beta	protein	357	22% helix, 40% strand	V5V7W3
P	DNA polymerase III subunit beta	protein	377	21% helix, 40% strand	V5V7W3

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains C, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	822	0.84	0.87	111	empty
2	1149	0.83	0.84	142	empty
3	870	0.79	0.82	95	empty
4	901	0.76	0.80	65	empty
5	1045	0.76	0.79	73	empty

Interfaces

34 interfaces between chains.

J–K · 1397 Å² buried · 16 hydrogen bonds · protein-protein
I–L · 1338 Å² buried · 12 hydrogen bonds · protein-protein
M–N · 1180 Å² buried · 16 hydrogen bonds · protein-protein
K–L · 1160 Å² buried · 19 hydrogen bonds · protein-protein
B–O · 1156 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6AP4 · Crystal structure of the DNA polymerase III subunit beta from Acinetobacter baumannii · 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 V5V7W3
Elsewhere: RCSB PDB 6AP4 · PDBe 6AP4 · UniProt V5V7W3

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