SMTL ID : 6g2w.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 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.207, I.241, V.270, P.271 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.241, A:V.270 MPD.2: 8 residues within 4Å: Chain A: L.57, L.121, D.122, I.124, A.125, I.170, I.171, D.172 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.57, A:I.124 Hydrogen bonds: A:D.172, A:D.172 MPD.3: 6 residues within 4Å: Chain A: D.213, F.216, L.217, R.275, F.278, M.282 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.213, A:F.216, A:L.217, A:R.275 Hydrogen bonds: A:R.275 MPD.4: 6 residues within 4Å: Chain A: V.39, C.77, P.113, C.114, N.158, F.160 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.113, A:N.158, A:F.160

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

DMS.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.6: 2 residues within 4Å: Chain A: N.222, G.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.222, A:G.223 Water bridges: A:R.195

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

ADP.7: 16 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, N.202, G.226, A.227, T.230 Ligands: NA.8 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, A:N.202 Salt bridges: A:K.66

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

NA.8: 4 residues within 4Å: Chain A: P.62, K.66, N.166 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.66, A:N.166, A:N.166

1 x AWD: ~{N}-(4-fluorophenyl)-4-methyl-piperazine-1-carboxamide(Non-covalent)

AWD.9: 6 residues within 4Å: Chain A: R.167, P.168, D.169, D.293, K.296, Y.297 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.297, A:Y.297 Hydrogen bonds: A:D.293

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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