SMTL ID : 4lg1.1

Human Methyltransferase-Like Protein 21D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

SAM.1: 18 residues within 4Å: Chain A: V.36, V.37, W.38, A.41, G.70, S.71, G.72, D.91, L.92, L.95, L.119, K.120, W.121, A.138, D.139, Y.142, Y.143, E.145 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.36, A:W.38, A:A.41, A:G.70, A:L.92, A:W.121, A:Y.143, A:Y.143, A:E.145 Water bridges: A:G.70, A:A.138 pi-Stacking: A:W.121, A:W.121, A:W.121 SAM.12: 18 residues within 4Å: Chain B: V.36, V.37, W.38, A.41, G.70, S.71, G.72, D.91, L.92, L.95, L.119, K.120, W.121, A.138, D.139, Y.142, Y.143, E.145 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:V.36, B:W.38, B:A.41, B:G.70, B:G.70, B:L.92, B:W.121, B:Y.143 Water bridges: B:G.70, B:A.138, B:Y.143 pi-Stacking: B:W.121, B:W.121, B:W.121 SAM.23: 18 residues within 4Å: Chain C: C.35, V.36, V.37, W.38, A.41, G.70, S.71, G.72, D.91, L.92, L.95, L.119, K.120, W.121, A.138, D.139, Y.142, Y.143 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:V.36, C:W.38, C:A.41, C:G.70, C:L.92, C:W.121, C:Y.143 Water bridges: C:K.120, C:A.138 pi-Stacking: C:W.121, C:W.121, C:W.121

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

EDO.2: 6 residues within 4Å: Chain A: K.195, L.198, S.207, E.208, I.210, H.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.195, A:L.198, A:I.210 EDO.13: 4 residues within 4Å: Chain B: R.18, E.49, S.54, H.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.54, B:S.54 Water bridges: B:D.19

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

UNX.3: 2 residues within 4Å: Chain A: A.58 Chain B: R.63 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: R.63, D.86 Chain B: R.64 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: V.66, V.88 Ligand excluded by PLIP UNX.6: 1 residues within 4Å: Chain A: K.120 Ligand excluded by PLIP UNX.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.10: 1 residues within 4Å: Chain A: Y.142 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: W.38, D.39 Ligand excluded by PLIP UNX.14: 2 residues within 4Å: Chain B: W.38, Y.142 Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain B: E.194 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain B: D.192, F.193 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain B: S.207, E.208 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: R.64 Chain B: R.63, D.86 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain B: T.50, K.200, H.201 Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Chain B: P.131 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain B: R.63, D.133 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain B: E.124 Ligand excluded by PLIP UNX.24: 1 residues within 4Å: Chain C: R.24 Ligand excluded by PLIP UNX.25: 2 residues within 4Å: Chain C: E.194, Y.214 Ligand excluded by PLIP UNX.26: 1 residues within 4Å: Chain C: S.207 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain C: D.192, F.193 Ligand excluded by PLIP UNX.28: 2 residues within 4Å: Chain C: L.92, K.120 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., The Crystal Structure of Human Methyltransferase-Like Protein 21D in Complex with SAM. To be Published

Release Date

2013-07-17

Peptides

Protein-lysine methyltransferase METTL21D: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Protein-lysine methyltransferase METTL21D

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