Research workbench

P97 variant 2 in the apo state

Analyse P97 variant 2 in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C19
Type: protein
Length: 4,191 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transitional endoplasmic reticulum ATPase
EC: 3.6.4.6
UniProt: P55072
Ligands: SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transitional endoplasmic reticulum ATPase (EC 3.6.4.6)	protein	734	37% helix, 16% strand	P55072
B	Transitional endoplasmic reticulum ATPase (EC 3.6.4.6)	protein	729	41% helix, 17% strand	P55072
C	Transitional endoplasmic reticulum ATPase (EC 3.6.4.6)	protein	729	42% helix, 17% strand	P55072
D	Transitional endoplasmic reticulum ATPase (EC 3.6.4.6)	protein	553	41% helix, 10% strand	P55072
E, F	Transitional endoplasmic reticulum ATPase (EC 3.6.4.6)	protein	723	42% helix, 17% strand	P55072

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F

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	870	0.85	0.87	106	SO4
2	623	0.83	0.87	89	empty
3	799	0.82	0.85	109	empty
4	628	0.82	0.87	82	empty
5	558	0.81	0.87	81	empty

Interfaces

10 interfaces between chains.

A–F · 3909 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 3821 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 3643 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 3638 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 3463 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5C19 · p97 variant 2 in the apo state · the same entry in another collection · chain C against C, 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 P55072
Elsewhere: RCSB PDB 5C19 · PDBe 5C19 · UniProt P55072

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