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Structure of T4 bacteriophage clamp loader bound to open clamp, DNA and ATP analog

Analyse Structure of T4 bacteriophage clamp loader bound to open clamp, DNA and ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U60
Type: protein + DNA
Length: 2,177 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase accessory protein 44; Template DNA strand; Primer DNA strand; DNA…
UniProt: P04526, P04527, P04525
Ligands: 08T, ADP, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 50% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	DNA polymerase accessory protein 44	protein	319	56% helix, 10% strand	P04526
C	DNA polymerase accessory protein 44	protein	320	56% helix, 11% strand	P04526
E	DNA polymerase accessory protein 44	protein	305	59% helix, 10% strand	P04526
I	Template DNA strand	dna	24	—	—
J	Primer DNA strand	dna	20	—	—
A	DNA polymerase accessory protein 62	protein	186	52% helix, 0% strand	P04527
G, H, F	DNA polymerase processivity component	protein	228	20% helix, 40% strand	P04525

Ligands and binding sites

08T · [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium · ligand · 3 copies · chains B, C, D, E
ADP · Adenosine-5'-diphosphate · ligand · chains E
MG · Magnesium ion · metal · 4 copies · chains B, C, D, E

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	936	0.84	0.86	91	ADP, MG
2	1113	0.84	0.85	133	empty
3	173	0.80	0.96	31	08T
4	158	0.80	0.96	31	08T
5	153	0.79	0.96	26	08T, MG

Interfaces

34 interfaces between chains.

B–C · 2384 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 2349 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2265 Å² buried · 37 hydrogen bonds · protein-protein
E–A · 1653 Å² buried · 22 hydrogen bonds · protein-protein
B–A · 1363 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

3U60 · Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog · the same entry in another collection · chain C against C, 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 P04526
Every structure of UniProt P04527
Every structure of UniProt P04525
Elsewhere: RCSB PDB 3U60 · PDBe 3U60 · UniProt P04526 · UniProt P04527 · UniProt P04525

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