SMTL ID : 8hl7.1

Crystal structure of p97 N/D1 in complex with a valosin-containing protein methyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 21 residues within 4Å: Chain A: G.25, V.27, V.28, W.29, A.32, G.61, S.62, G.63, T.64, D.82, L.83, L.86, L.110, K.111, W.112, A.129, D.130, Y.133, Y.134, E.136 Chain B: K.293 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.29, A:A.32, A:G.61, A:W.112, A:Y.134, A:E.136 pi-Stacking: A:W.112, A:W.112, A:W.112, B:H.295

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.4, V.5, L.6, E.7, K.37, Y.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.4, A:E.7, A:K.37, A:K.37 GOL.3: 8 residues within 4Å: Chain A: R.4, V.28, W.29, D.30, E.160 Chain B: S.304, L.307, A.334 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.4, A:D.30, A:E.160, B:R.337 Water bridges: A:V.28, B:T.308 GOL.8: 3 residues within 4Å: Chain B: Y.116, V.132, R.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.133

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 3 residues within 4Å: Chain A: E.195, R.197 Chain B: F.338 No protein-ligand interaction detected (PLIP) FMT.7: 4 residues within 4Å: Chain B: E.12, N.14, N.63, R.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.63

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 7 residues within 4Å: Chain A: R.9, T.41, P.42, E.190, K.191, H.192, E.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.194, A:E.194 Salt bridges: A:R.9

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

ADP.6: 16 residues within 4Å: Chain B: D.183, I.184, G.185, P.224, P.225, G.226, T.227, G.228, K.229, T.230, L.231, D.282, I.358, H.362, G.386, A.387 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.185, B:G.185, B:G.226, B:T.227, B:G.228, B:K.229, B:T.230, B:T.230, B:T.230, B:L.231, B:D.282, B:G.386 Salt bridges: B:K.229

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.9: 8 residues within 4Å: Chain B: E.8, A.9, E.12, M.62, N.63, R.64, R.67, S.254 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.9, B:R.64, B:S.254 Salt bridges: B:E.8, B:E.8, B:E.12, B:E.12, B:R.64, B:R.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, T.Q. et al., Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase. Iscience (2023)

Release Date

2023-07-12

Peptides

Protein N-lysine methyltransferase METTL21D: A
Transitional endoplasmic reticulum ATPase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein N-lysine methyltransferase METTL21D

Transitional endoplasmic reticulum ATPase