MolNFT v1 · #169172 · protein

Pig R615C RYR1 egta (all classes, open)

6X34 · Peptidyl-prolyl cis-trans isomerase FKBP1B: “Pig R615C RYR1 egta (all classes, open)”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #169172 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6X34
Type: protein
Length: 15,272 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidyl-prolyl cis-trans isomerase FKBP1B; Ryanodine receptor
EC: 5.2.1.8
UniProt: P68106
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 3 distinct chains · 48% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Peptidyl-prolyl cis-trans isomerase FKBP1B (EC 5.2.1.8)	protein	103	12% helix, 26% strand	P68106
B, D, H	Ryanodine receptor	protein	3715	49% helix, 10% strand	—
F	Ryanodine receptor	protein	3715	49% helix, 10% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains B, D, F, H

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

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	854	0.87	0.88	97	empty
2	873	0.86	0.88	91	empty
3	868	0.86	0.88	90	empty
4	909	0.86	0.87	96	empty
5	873	0.86	0.88	124	empty

Interfaces

8 interfaces between chains.

B–H · 1962 Å² buried · 5 hydrogen bonds · protein-protein
D–F · 1960 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 1958 Å² buried · 5 hydrogen bonds · protein-protein
F–H · 1956 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 1284 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6X34 · Pig R615C RyR1 EGTA (all classes, open) · the same entry in another collection · chain G against G, TM-score 1.00
P68106 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1B (P68106) · a predicted model of the same protein · chain G against A, TM-score 0.93

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 P68106
Elsewhere: RCSB PDB 6X34 · PDBe 6X34 · UniProt P68106

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