SMTL ID : 4qqk.1

Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) with GMS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x 37H: (5S)-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}-N~6~-carbamimidoyl-L-lysine(Non-covalent)

37H.1: 23 residues within 4Å: Chain A: H.58, M.61, R.67, G.91, A.92, G.93, I.96, L.97, V.112, E.113, A.114, S.115, G.139, P.140, V.141, E.142, E.156, W.157, M.158, M.167, S.170 Ligands: UNX.8, UNX.20 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:H.58, A:G.91, A:G.93, A:A.114, A:V.141, A:E.142, A:M.158, A:M.158, A:S.170 Water bridges: A:S.115, A:S.115 Salt bridges: A:R.67, A:E.156 37H.24: 23 residues within 4Å: Chain B: H.58, M.61, R.67, G.91, A.92, G.93, I.96, L.97, V.112, E.113, A.114, S.115, G.139, P.140, V.141, E.142, E.156, W.157, M.158, M.167, S.170 Ligands: UNX.31, UNX.43 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:H.58, B:G.91, B:G.93, B:A.114, B:V.141, B:E.142, B:M.158, B:M.158, B:S.170 Water bridges: B:S.115, B:S.115 Salt bridges: B:R.67, B:E.156

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: R.275, S.339, G.340, E.341, R.359, Y.360, K.361, E.367 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.275, A:R.275, A:S.339, A:E.367 GOL.25: 8 residues within 4Å: Chain B: R.275, S.339, G.340, E.341, R.359, Y.360, K.361, E.367 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.275, B:R.275, B:S.339, B:E.367

42 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 4 residues within 4Å: Chain A: G.273, G.274, I.342, T.343 Ligand excluded by PLIP UNX.4: 1 residues within 4Å: Chain A: V.239 Ligand excluded by PLIP UNX.5: 1 residues within 4Å: Chain A: Y.160 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: L.163, P.346, P.351 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: P.251, Q.252, R.253 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: H.318, W.319 Ligands: 37H.1 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: G.233 Chain B: E.50 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: S.347, R.353, M.374 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: L.231, H.234, Y.325 Ligand excluded by PLIP UNX.12: 1 residues within 4Å: Chain A: M.201 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: T.296, F.297, P.298 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: E.341, L.357, L.358, R.359 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: G.274, R.275 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: L.163, S.166 Ligand excluded by PLIP UNX.17: 1 residues within 4Å: Chain A: D.335 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: R.250, Q.252 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: R.253, F.254, A.255 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain A: V.57 Ligands: 37H.1 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: G.300, E.303 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain A: Q.120 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: R.175, T.176, L.179 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain B: G.273, G.274, I.342, T.343 Ligand excluded by PLIP UNX.27: 1 residues within 4Å: Chain B: V.239 Ligand excluded by PLIP UNX.28: 1 residues within 4Å: Chain B: Y.160 Ligand excluded by PLIP UNX.29: 3 residues within 4Å: Chain B: L.163, P.346, P.351 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain B: P.251, Q.252, R.253 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain B: H.318, W.319 Ligands: 37H.24 Ligand excluded by PLIP UNX.32: 2 residues within 4Å: Chain A: E.50 Chain B: G.233 Ligand excluded by PLIP UNX.33: 3 residues within 4Å: Chain B: S.347, R.353, M.374 Ligand excluded by PLIP UNX.34: 3 residues within 4Å: Chain B: L.231, H.234, Y.325 Ligand excluded by PLIP UNX.35: 1 residues within 4Å: Chain B: M.201 Ligand excluded by PLIP UNX.36: 3 residues within 4Å: Chain B: T.296, F.297, P.298 Ligand excluded by PLIP UNX.37: 4 residues within 4Å: Chain B: E.341, L.357, L.358, R.359 Ligand excluded by PLIP UNX.38: 2 residues within 4Å: Chain B: G.274, R.275 Ligand excluded by PLIP UNX.39: 2 residues within 4Å: Chain B: L.163, S.166 Ligand excluded by PLIP UNX.40: 1 residues within 4Å: Chain B: D.335 Ligand excluded by PLIP UNX.41: 2 residues within 4Å: Chain B: R.250, Q.252 Ligand excluded by PLIP UNX.42: 3 residues within 4Å: Chain B: R.253, F.254, A.255 Ligand excluded by PLIP UNX.43: 2 residues within 4Å: Chain B: V.57 Ligands: 37H.24 Ligand excluded by PLIP UNX.44: 2 residues within 4Å: Chain B: G.300, E.303 Ligand excluded by PLIP UNX.45: 1 residues within 4Å: Chain B: Q.120 Ligand excluded by PLIP UNX.46: 3 residues within 4Å: Chain B: R.175, T.176, L.179 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, H. et al., Structural basis of arginine asymmetrical dimethylation by PRMT6. Biochem. J. (2016)

Release Date

2014-07-16

Peptides

Protein arginine N-methyltransferase 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein arginine N-methyltransferase 6

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