Research workbench

X-ray crystal structure of plyc

Analyse X-ray crystal structure of plyc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4F88
Type: protein
Length: 1,827 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plyca; Plycb
UniProt: Q7Y3F1, Q7Y3F3
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 15 distinct chains · 32% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Plyca	protein	430	39% helix, 9% strand	Q7Y3F1
2	Plyca	protein	418	41% helix, 7% strand	Q7Y3F1
A	Plycb	protein	68	22% helix, 29% strand	Q7Y3F3
B	Plycb	protein	69	22% helix, 29% strand	Q7Y3F3
C, G	Plycb	protein	69	22% helix, 29% strand	Q7Y3F3
D	Plycb	protein	63	29% helix, 29% strand	Q7Y3F3
E, F, M	Plycb	protein	65	23% helix, 25% strand	Q7Y3F3
H	Plycb	protein	67	22% helix, 30% strand	Q7Y3F3
I	Plycb	protein	52	23% helix, 10% strand	Q7Y3F3
J	Plycb	protein	35	29% helix, 6% strand	Q7Y3F3
K	Plycb	protein	53	21% helix, 4% strand	Q7Y3F3
L	Plycb	protein	55	25% helix, 0% strand	Q7Y3F3
N	Plycb	protein	59	25% helix, 27% strand	Q7Y3F3
O	Plycb	protein	65	23% helix, 25% strand	Q7Y3F3
P	Plycb	protein	60	25% helix, 27% strand	Q7Y3F3

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	887	0.81	0.83	94	empty
2	215	0.77	0.91	32	empty
3	253	0.75	0.88	43	empty
4	364	0.73	0.84	53	empty
5	714	0.72	0.79	56	empty

Interfaces

39 interfaces between chains.

B–C · 1145 Å² buried · 20 hydrogen bonds · protein-protein
A–H · 1033 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1008 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 991 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 810 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4F88 · X-ray Crystal Structure of PlyC · the same entry in another collection · chain 1 against 1, 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 Q7Y3F1
Every structure of UniProt Q7Y3F3
Elsewhere: RCSB PDB 4F88 · PDBe 4F88 · UniProt Q7Y3F1 · UniProt Q7Y3F3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.