MolNFT v1 · #176447 · protein

Acidic stable capsid structure of helicobacter pylori bacteriophage KHP30

7DN2 · Major structural protein ORF14: “Acidic stable capsid structure of helicobacter pylori bacteriophage KHP30”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #176447 on GenesisL1: 3D structure, binding sites and…

PDB: 7DN2
Type: protein
Length: 4,441 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major structural protein ORF14; Cement protein GP15
UniProt: I7H0H9, I7HFW5
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 9 distinct chains · 23% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	Major structural protein ORF14	protein	368	23% helix, 31% strand	I7H0H9
b	Major structural protein ORF14	protein	366	26% helix, 28% strand	I7H0H9
c	Major structural protein ORF14	protein	368	24% helix, 32% strand	I7H0H9
d	Major structural protein ORF14	protein	371	23% helix, 31% strand	I7H0H9
e, f	Major structural protein ORF14	protein	370	24% helix, 29% strand	I7H0H9
g	Major structural protein ORF14	protein	370	25% helix, 28% strand	I7H0H9
h	Major structural protein ORF14	protein	362	24% helix, 31% strand	I7H0H9
i	Major structural protein ORF14	protein	362	21% helix, 25% strand	I7H0H9
1, 2, 3, 4, 5, 6, 7, 8, 9	Cement protein GP15	protein	126	3% helix, 54% strand	I7HFW5

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	131	0.79	0.97	35	empty
2	867	0.79	0.82	95	empty
3	523	0.79	0.85	62	empty
4	124	0.78	0.97	24	empty
5	104	0.78	0.98	29	empty

Interfaces

51 interfaces between chains.

b–c · 3620 Å² buried · 34 hydrogen bonds · protein-protein
g–h · 3574 Å² buried · 26 hydrogen bonds · protein-protein
e–f · 3521 Å² buried · 32 hydrogen bonds · protein-protein
a–b · 3505 Å² buried · 32 hydrogen bonds · protein-protein
d–e · 3475 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

7DN2 · Acidic stable capsid structure of Helicobacter pylori bacteriophage KHP30 · the same entry in another collection · chain 3 against 3, 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 I7H0H9
Every structure of UniProt I7HFW5
Elsewhere: RCSB PDB 7DN2 · PDBe 7DN2 · UniProt I7H0H9 · UniProt I7HFW5

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