MolNFT v1 · #21239 · protein

Crystal structure of aaa ATPase P97/VCP ND1 in complex with P47 C

1S3S · Transitional endoplasmic reticulum ATPase (ter ATPase) (15S…: “Crystal structure of aaa ATPase P97/VCP ND1 in complex with P47 C”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.82). MolNFT v1 #21239 on…

PDB: 1S3S
Type: protein
Length: 2,871 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transitional endoplasmic reticulum ATPase (ter ATPase) (15S MG(2+)- ATPase P97 subunit)…
UniProt: Q01853, O35987
Ligands: ADP
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	Transitional endoplasmic reticulum ATPase (ter ATPase) (15S MG(2+)- ATPase P97 subunit) (valosin containing protein) (vcp) [contains: valosin]	protein	436	36% helix, 23% strand	Q01853
C	Transitional endoplasmic reticulum ATPase (ter ATPase) (15S MG(2+)- ATPase P97 subunit) (valosin containing protein) (vcp) [contains: valosin]	protein	437	38% helix, 23% strand	Q01853
F	Transitional endoplasmic reticulum ATPase (ter ATPase) (15S MG(2+)- ATPase P97 subunit) (valosin containing protein) (vcp) [contains: valosin]	protein	441	37% helix, 24% strand	Q01853
G	P47 protein	protein	118	25% helix, 21% strand	O35987
H	P47 protein	protein	107	26% helix, 21% strand	O35987
I	P47 protein	protein	24	46% helix, 0% strand	O35987

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, E, B, F, C, D

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	1147	0.82	0.83	126	ADP
2	1179	0.81	0.82	116	ADP
3	1046	0.81	0.82	118	ADP
4	1057	0.81	0.82	118	ADP
5	1074	0.79	0.81	111	ADP

Interfaces

8 interfaces between chains.

A–F · 1662 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 1649 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 1599 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 1488 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 1441 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

1S3S · Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C · the same entry in another collection · chain H against H, TM-score 1.00
Q01853 · AlphaFold monomer V2.0 prediction for transitional endoplasmic reticulum ATPase (Q01853) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q01853
Every structure of UniProt O35987
Elsewhere: RCSB PDB 1S3S · PDBe 1S3S · UniProt Q01853 · UniProt O35987

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