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The crystal structure of wild type pa endonuclease (2009/H1N1/CALIFORNIA) in complex with raltegravir

Analyse The crystal structure of wild type pa endonuclease (2009/H1N1/CALIFORNIA) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7M0N
Type: protein
Length: 737 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein pa-X
UniProt: C6Y633
Ligands: RLT, MN, SO4
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein pa-X	protein	184	57% helix, 13% strand	C6Y633
B, D	Protein pa-X	protein	183	56% helix, 13% strand	C6Y633
C	Protein pa-X	protein	187	56% helix, 12% strand	C6Y633

Ligands and binding sites

RLT · N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl) carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide · ligand · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
GOL · Glycerol · additive · 5 copies · chains B, D

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

Pockets

8 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	610	0.68	0.77	50	RLT, MN
2	507	0.67	0.78	41	RLT, MN
3	520	0.66	0.77	42	RLT, MN
4	446	0.64	0.77	42	RLT, MN
5	103	0.37	0.75	19	empty

Interfaces

4 interfaces between chains.

A–C · 636 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 619 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 585 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 582 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7M0N · The crystal structure of wild type PA endonuclease (A/Vietnam/1203/2004) in complex with… · 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 C6Y633
Elsewhere: RCSB PDB 7M0N · PDBe 7M0N · UniProt C6Y633

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