SMTL ID : 6g2y.1

Crystal structure of the p97 D2 domain in a helical split-washer conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 4 residues within 4Å: Chain A: P.204, I.238, V.267, P.268 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.238, A:V.267 MPD.2: 7 residues within 4Å: Chain A: L.54, L.118, A.122, I.140, I.167, I.168, D.169 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.54, A:I.140 Hydrogen bonds: A:L.118, A:D.169 MPD.3: 5 residues within 4Å: Chain A: D.210, F.213, L.214, R.272, F.275 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.213, A:F.213, A:R.272, A:F.275 Hydrogen bonds: A:R.272 MPD.4: 4 residues within 4Å: Chain A: C.74, P.110, C.111, N.155 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.110

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: P.187, D.188, N.219, G.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.220 Water bridges: A:R.192

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 16 residues within 4Å: Chain A: D.17, I.18, G.19, P.59, G.60, C.61, G.62, K.63, T.64, L.65, I.195, N.199, G.223, A.224, T.227 Ligands: NA.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.19, A:G.60, A:C.61, A:C.61, A:G.62, A:K.63, A:T.64, A:T.64, A:T.64, A:L.65 Salt bridges: A:K.63

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: P.59, K.63, N.163 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.63, A:N.163, A:N.163

1 x ELQ: [3,4-bis(fluoranyl)phenyl]-(4-methylpiperazin-1-yl)methanone(Non-covalent)

ELQ.9: 6 residues within 4Å: Chain A: R.164, P.165, D.166, D.290, K.293, Y.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.293, A:K.293, A:Y.294 Salt bridges: A:D.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stach, L. et al., Crystal structure of the catalytic D2 domain of the AAA+ ATPase p97 reveals a putative helical split-washer-type mechanism for substrate unfolding. Febs Lett. (2020)

Release Date

2019-04-10

Peptides

Transitional endoplasmic reticulum ATPase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Transitional endoplasmic reticulum ATPase