SMTL ID : 7l1g.1

PRMT5-MEP50 Complexed with SAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: W.194, D.227, R.228, L.230, S.484, H.518, T.554 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.194, A:R.228, A:S.484, A:H.518 EDO.2: 4 residues within 4Å: Chain A: S.329, Q.330, E.333, R.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.333, A:R.376 EDO.3: 5 residues within 4Å: Chain A: F.48, T.88, V.91, W.160, Q.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.271 EDO.4: 6 residues within 4Å: Chain A: L.316, Q.317, S.318, C.495, Y.510 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.318 Water bridges: A:S.318 EDO.5: 5 residues within 4Å: Chain A: A.494, C.495, R.496, E.497 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: E.137, D.138, N.139, T.140, N.199, L.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.138, A:N.139, A:T.140, A:T.140 EDO.7: 4 residues within 4Å: Chain A: F.54, Q.74, Q.117, F.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117 EDO.8: 5 residues within 4Å: Chain A: E.336, R.376, G.377, P.378, W.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.377 EDO.9: 4 residues within 4Å: Chain A: E.400, K.401, S.425, S.426 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.425 Water bridges: A:S.426, A:D.427 EDO.10: 4 residues within 4Å: Chain A: I.150, H.154, S.207, R.209 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain A: Y.543, C.544, T.545 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.545 EDO.15: 2 residues within 4Å: Chain B: D.134, K.153 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.162, A:R.162, A:R.162 EDO.16: 8 residues within 4Å: Chain B: N.198, I.200, G.215, C.216, P.219, Y.221, P.223, F.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.216, B:Y.221 EDO.17: 4 residues within 4Å: Chain B: V.141, L.142, S.143, G.145 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain B: D.93, S.137, T.138, C.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.137 Water bridges: B:L.226, B:L.269

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain A: L.134, N.135, R.162, P.164 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: I.226, W.229, L.230, R.264 Ligand excluded by PLIP

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.14: 20 residues within 4Å: Chain A: P.322, L.323, Y.332, F.335, K.341, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, L.445, E.452, C.457, W.587 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.375, A:K.401, A:D.427, A:M.428 Water bridges: A:N.402 Salt bridges: A:K.341, A:E.443 pi-Cation interactions: A:K.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Candito, D.A. et al., Development of a Flexible and Robust Synthesis of Tetrahydrofuro[3,4- b ]furan Nucleoside Analogues. J.Org.Chem. (2021)

Release Date

2021-04-14

Peptides

Protein arginine N-methyltransferase 5: A
Methylosome protein 50: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein arginine N-methyltransferase 5

Methylosome protein 50

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