SMTL ID : 6g2x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

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

MPD.1: 5 residues within 4Å: Chain A: P.207, I.241, V.270, P.271, I.273 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.241, A:V.270, A:I.273 Hydrogen bonds: A:P.271 MPD.2: 8 residues within 4Å: Chain A: L.57, L.121, D.122, A.125, I.143, I.170, I.171, D.172 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.57, A:I.143, A:I.171 Hydrogen bonds: A:D.172 MPD.3: 5 residues within 4Å: Chain A: D.213, F.216, L.217, R.275, F.278 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.213, A:F.216, A:R.275, A:F.278 Hydrogen bonds: A:R.275 MPD.4: 4 residues within 4Å: Chain A: C.77, P.113, C.114, N.158 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.113, A:N.158

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

DMS.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.6: 5 residues within 4Å: Chain A: L.189, P.190, D.191, N.222, G.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.223 Water bridges: A:R.195

2 x EJQ: ~{N}-(4-fluorophenyl)-2-pyrrolidin-1-yl-ethanamide(Non-covalent)

EJQ.7: 8 residues within 4Å: Chain A: R.167, P.168, D.169, D.293, K.296, Y.297, F.300 Ligands: EJQ.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.296, A:K.296 Water bridges: A:Y.297 Salt bridges: A:D.293 pi-Stacking: A:Y.297 EJQ.8: 7 residues within 4Å: Chain A: D.169, K.296, M.299, F.300, T.303, L.304 Ligands: EJQ.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.169, A:L.304 Hydrogen bonds: A:T.303

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

ADP.9: 15 residues within 4Å: Chain A: D.20, I.21, G.22, P.62, G.63, C.64, G.65, K.66, T.67, L.68, I.198, G.226, A.227, T.230 Ligands: NA.10 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.22, A:G.63, A:C.64, A:C.64, A:G.65, A:K.66, A:T.67, A:T.67, A:T.67, A:L.68 Water bridges: A:T.67 Salt bridges: A:K.66

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

NA.10: 4 residues within 4Å: Chain A: P.62, K.66, N.166 Ligands: ADP.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.66, A:N.166, A:N.166

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

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