MolNFT v1 · #18084 · protein

Fitting of GP8 structure into the cryoem reconstruction of the bacteriophage T4 baseplate

1PDM · Baseplate structural protein GP8: “Fitting of GP8 structure into the cryoem reconstruction of the bacteriophage T4 baseplate”. Electron microscopy, 3 pockets (best druggability 0.31). MolNFT v1 #18084 on GenesisL1: 3D structure…

PDB: 1PDM
Type: protein
Length: 3,936 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Baseplate structural protein GP8
UniProt: P19062
Pockets: 3 · best druggability 0.31

Structure

electron microscopy · 1 distinct chain · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Baseplate structural protein GP8	protein	328	0% helix, 0% strand	P19062

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.31	0.73	23	empty
2	66	0.29	0.72	21	empty
3	52	0.28	0.73	17	empty

Interfaces

6 interfaces between chains.

I–J · 387 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 386 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 386 Å² buried · 0 hydrogen bonds · protein-protein
E–F · 384 Å² buried · 0 hydrogen bonds · protein-protein
K–L · 382 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1PDM · Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate · 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 P19062
Elsewhere: RCSB PDB 1PDM · PDBe 1PDM · UniProt P19062

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