SMTL ID : 7twu.1

Crystal structure of human phenylethanolamine N-methyltransferase (PNMT) in complex with (2S)-2-amino-4-(((5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(4-(7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl)butyl)amino)butanoic acid and AdoHcy (SAH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: Y.39, Y.47, Y.52, G.91, S.92, G.93, T.95, Y.97, D.113, F.114, L.115, N.118, D.170, V.171, H.172, A.193, F.194, C.195, V.199, Y.234 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.47 Hydrogen bonds: A:Y.47, A:G.91, A:N.118, A:D.170, A:V.171, A:A.193 Salt bridges: A:K.69 pi-Stacking: A:Y.39

1 x CD: CADMIUM ION(Non-covalent)

CD.2: 2 residues within 4Å: Chain A: K.69, F.194 No protein-ligand interaction detected (PLIP)

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Ligands: EDO.5, EDO.7 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: C.72, T.76, D.264, R.266, F.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.264 EDO.5: 1 residues within 4Å: Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: E.230, P.245, E.250 Chain B: N.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.230, A:S.247 EDO.7: 2 residues within 4Å: Chain A: I.145 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: P.55, D.58, N.61, G.64, H.273, L.274 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.55, A:N.61 Water bridges: A:N.63, A:H.273 EDO.9: 3 residues within 4Å: Chain A: R.45, P.130, G.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.45 EDO.10: 7 residues within 4Å: Chain A: Y.47, F.194, E.197, A.198, A.228, E.231, Y.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.194 Water bridges: A:N.51, A:D.279 EDO.11: 5 residues within 4Å: Chain A: W.68, R.71, Q.75, R.266 Chain B: E.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.71, A:R.266 EDO.13: 1 residues within 4Å: Chain B: K.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.148 Water bridges: B:D.154 EDO.14: 5 residues within 4Å: Chain B: Q.75, T.76, D.264, R.266, W.288 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.76, B:D.264, B:R.266 EDO.15: 1 residues within 4Å: Chain B: P.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.176 EDO.16: 3 residues within 4Å: Chain B: F.114, L.115, E.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.116 EDO.17: 2 residues within 4Å: Chain B: R.157, Q.158 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.158 EDO.18: 3 residues within 4Å: Chain B: C.60, N.61, P.62 No protein-ligand interaction detected (PLIP)

1 x KNX: 5'-([(3S)-3-amino-3-carboxypropyl]{4-[(4R)-7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl]butyl}amino)-5'-deoxyadenosine(Non-covalent)

KNX.12: 30 residues within 4Å: Chain B: Y.39, Y.47, N.51, Y.52, R.56, K.69, G.91, S.92, G.93, T.95, Y.97, D.113, F.114, L.115, N.118, I.169, D.170, V.171, H.172, A.193, F.194, C.195, A.198, V.199, E.231, Y.234, M.270, D.279, V.281, V.284 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.47, B:F.194, B:A.198, B:Y.234 Hydrogen bonds: B:Y.47, B:Y.52, B:T.95, B:Y.97, B:L.115, B:N.118, B:D.170, B:D.170, B:V.171, B:A.193, B:D.279, B:D.279 Water bridges: B:A.193 pi-Stacking: B:Y.39, B:F.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahmoodi, N. et al., Cell-Effective Transition-State Analogue of Phenylethanolamine N -Methyltransferase. Biochemistry (2023)

Release Date

2023-02-15

Peptides

Phenylethanolamine N-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phenylethanolamine N-methyltransferase

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