Research workbench

DLP 5 FOLD

Analyse DLP 5 FOLD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XF8
Type: protein
Length: 6,094 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer capsid protein mu-1; Outer capsid protein sigma-3; Inner capsid protein sigma-2…
EC: 3.6.4.13, 2.1.1.56, 2.7.7.50
UniProt: P11077, P07939, P11314, Q9WAB2, Q91RA5
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 6 distinct chains · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K, F	Outer capsid protein mu-1	protein	608	39% helix, 15% strand	P11077
I, H, G	Outer capsid protein sigma-3	protein	365	42% helix, 13% strand	P07939
E	Inner capsid protein sigma-2	protein	417	46% helix, 10% strand	P11314
C	Inner capsid protein lambda-1 (EC 3.6.4.13)	protein	1051	35% helix, 16% strand	Q9WAB2
B	Inner capsid protein lambda-1 (EC 3.6.4.13)	protein	1031	39% helix, 15% strand	Q9WAB2
A	MRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56, 2.7.7.50)	protein	1284	26% helix, 23% strand	Q91RA5

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	798	0.87	0.90	121	empty
2	526	0.86	0.92	79	empty
3	933	0.86	0.87	123	empty
4	603	0.84	0.89	94	empty
5	592	0.84	0.89	92	empty

Interfaces

14 interfaces between chains.

K–F · 3154 Å² buried · 31 hydrogen bonds · protein-protein
E–B · 1994 Å² buried · 35 hydrogen bonds · protein-protein
C–B · 1871 Å² buried · 56 hydrogen bonds · protein-protein
K–G · 1161 Å² buried · 84 hydrogen bonds · protein-protein
I–F · 1099 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6XF8 · DLP 5 fold · the same entry in another collection · chain F against F, 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 P11077
Every structure of UniProt P07939
Every structure of UniProt P11314
Every structure of UniProt Q9WAB2
Every structure of UniProt Q91RA5
Elsewhere: RCSB PDB 6XF8 · PDBe 6XF8 · UniProt P11077 · UniProt P07939 · UniProt P11314 · UniProt Q9WAB2 · UniProt Q91RA5

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