SMTL ID : 4pwy.1

Crystal structure of a Calmodulin-lysine N-methyltransferase fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 21 residues within 4Å: Chain A: W.69, E.72, G.95, G.96, G.97, D.119, G.120, N.121, L.151, R.152, W.153, D.154, A.172, D.173, C.174, F.176, L.177, Y.180 Chain B: R.4, F.60 Ligands: GOL.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.72, A:E.72, A:G.95, A:G.97, A:G.120, A:N.121, A:W.153, A:D.154, A:A.172 Water bridges: A:G.95, A:N.121, A:A.172 pi-Stacking: A:W.153, A:W.153, A:W.153, B:F.60 Salt bridges: B:R.4 SAH.24: 21 residues within 4Å: Chain A: R.4, F.60 Chain B: W.69, E.72, G.95, G.96, G.97, D.119, G.120, N.121, L.151, R.152, W.153, D.154, A.172, D.173, C.174, F.176, L.177, Y.180 Ligands: GOL.25 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain B Salt bridges: A:R.4 pi-Stacking: A:F.60, B:W.153, B:W.153, B:W.153 Hydrogen bonds: B:E.72, B:G.95, B:G.97, B:G.120, B:N.121, B:W.153, B:D.154, B:D.154, B:A.172 Water bridges: B:G.95, B:N.121, B:A.172

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: C.67, I.68, W.69, E.72, G.96, G.97, M.98, T.99, C.100 Ligands: SAH.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.69, A:M.98, A:T.99, A:T.99, A:C.100 GOL.23: 6 residues within 4Å: Chain A: R.5 Chain B: E.7, V.66, I.68, W.69, P.70 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.5, A:R.5, B:E.7, B:E.7 Water bridges: B:F.6 GOL.25: 10 residues within 4Å: Chain B: C.67, I.68, W.69, E.72, G.96, G.97, M.98, T.99, C.100 Ligands: SAH.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.69, B:M.98, B:T.99, B:T.99, B:C.100 GOL.46: 6 residues within 4Å: Chain A: E.7, V.66, I.68, W.69, P.70 Chain B: R.5 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.7, B:R.5, B:R.5 Water bridges: A:F.6

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

UNX.3: 4 residues within 4Å: Chain A: Q.211, N.214, L.215 Ligands: UNX.4 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: Q.211 Ligands: UNX.3, UNX.5 Ligand excluded by PLIP UNX.5: 4 residues within 4Å: Chain A: R.181, Q.211, L.215 Ligands: UNX.4 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: H.232, N.235 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: E.227, E.250 Ligand excluded by PLIP UNX.8: 5 residues within 4Å: Chain A: R.5, F.6, E.7, S.8 Ligands: UNX.21 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: R.4 Chain B: W.69 Ligand excluded by PLIP UNX.10: 1 residues within 4Å: Chain A: D.111 Ligand excluded by PLIP UNX.11: 4 residues within 4Å: Chain A: N.83, S.109, D.111, K.142 Ligand excluded by PLIP UNX.12: 4 residues within 4Å: Chain A: W.153, D.154, D.186 Ligands: UNX.15 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: D.154, N.155, E.156 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: H.226, E.227, N.228 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: D.154, E.156 Ligands: UNX.12 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: R.204, E.250, N.251 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: A.182, S.183 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: T.15, G.17, W.29 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: D.230, E.231 Ligand excluded by PLIP UNX.20: 4 residues within 4Å: Chain A: N.10, L.11, F.12, E.73 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Chain A: S.8, N.10 Ligands: UNX.8 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain B: Q.211, N.214, L.215 Ligands: UNX.27 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain B: Q.211 Ligands: UNX.26, UNX.28 Ligand excluded by PLIP UNX.28: 4 residues within 4Å: Chain B: R.181, Q.211, L.215 Ligands: UNX.27 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain B: H.232, N.235 Ligand excluded by PLIP UNX.30: 2 residues within 4Å: Chain B: E.227, E.250 Ligand excluded by PLIP UNX.31: 5 residues within 4Å: Chain B: R.5, F.6, E.7, S.8 Ligands: UNX.44 Ligand excluded by PLIP UNX.32: 2 residues within 4Å: Chain A: W.69 Chain B: R.4 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Chain B: D.111 Ligand excluded by PLIP UNX.34: 4 residues within 4Å: Chain B: N.83, S.109, D.111, K.142 Ligand excluded by PLIP UNX.35: 4 residues within 4Å: Chain B: W.153, D.154, D.186 Ligands: UNX.38 Ligand excluded by PLIP UNX.36: 3 residues within 4Å: Chain B: D.154, N.155, E.156 Ligand excluded by PLIP UNX.37: 3 residues within 4Å: Chain B: H.226, E.227, N.228 Ligand excluded by PLIP UNX.38: 3 residues within 4Å: Chain B: D.154, E.156 Ligands: UNX.35 Ligand excluded by PLIP UNX.39: 3 residues within 4Å: Chain B: R.204, E.250, N.251 Ligand excluded by PLIP UNX.40: 2 residues within 4Å: Chain B: A.182, S.183 Ligand excluded by PLIP UNX.41: 3 residues within 4Å: Chain B: T.15, G.17, W.29 Ligand excluded by PLIP UNX.42: 2 residues within 4Å: Chain B: D.230, E.231 Ligand excluded by PLIP UNX.43: 4 residues within 4Å: Chain B: N.10, L.11, F.12, E.73 Ligand excluded by PLIP UNX.44: 3 residues within 4Å: Chain B: S.8, N.10 Ligands: UNX.31 Ligand excluded by PLIP

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.22: 7 residues within 4Å: Chain A: R.5, L.252, H.253 Chain B: R.5, L.252, H.253 Ligands: MLI.45 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Water bridges: A:R.5, A:R.205, B:R.5, B:R.205, B:H.253 Salt bridges: A:R.5, A:R.5, A:H.253, B:R.5, B:R.5, B:H.253 Hydrophobic interactions: B:L.252 MLI.45: 7 residues within 4Å: Chain A: R.5, L.252, H.253 Chain B: R.5, L.252, H.253 Ligands: MLI.22 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.252 Water bridges: A:R.5, A:R.205, A:H.253, B:R.5, B:R.205 Salt bridges: A:R.5, A:R.5, A:H.253, B:R.5, B:R.5, B:H.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tempel, W. et al., Crystal structure of a Calmodulin-lysine N-methyltransferase fragment. TO BE PUBLISHED

Release Date

2014-04-16

Peptides

Calmodulin-lysine N-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Calmodulin-lysine N-methyltransferase