SMTL ID : 8zjv.2 (1 other biounit)

Crystal Structure of the ERK2 complexed with 5-Iodotubercidin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 5ID: (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL(Non-covalent)

5ID.1: 15 residues within 4Å: Chain A: I.22, G.23, E.24, V.30, A.43, Q.96, D.97, L.98, M.99, D.102, K.105, S.144, L.147, D.158 Ligands: EDO.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:D.97, A:M.99 Water bridges: A:K.45, A:K.45, A:T.101, A:D.158, A:D.158 5ID.10: 15 residues within 4Å: Chain B: I.22, G.23, E.24, V.30, A.43, Q.96, D.97, L.98, M.99, D.102, K.105, S.144, L.147, D.158 Ligands: EDO.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.147 Hydrogen bonds: B:D.97, B:M.99, B:D.102 Water bridges: B:K.45, B:K.45, B:T.101, B:S.144, B:S.144

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

EDO.2: 1 residues within 4Å: Chain A: K.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.142 Water bridges: A:D.140, A:D.140, A:D.158, A:D.158 EDO.3: 5 residues within 4Å: Chain A: G.25, A.26, Y.27, G.28, K.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.25, A:Y.27, A:K.45 Water bridges: A:K.45 EDO.4: 5 residues within 4Å: Chain A: D.102, Y.104, K.105, S.144 Ligands: 5ID.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.105, A:K.105 Water bridges: A:E.24 EDO.11: 1 residues within 4Å: Chain B: K.142 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.142 Water bridges: B:D.140, B:D.158 EDO.12: 5 residues within 4Å: Chain B: G.25, A.26, Y.27, G.28, K.45 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.25, B:Y.27, B:K.45 Water bridges: B:K.45 EDO.13: 5 residues within 4Å: Chain B: D.102, Y.104, K.105, S.144 Ligands: 5ID.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.105, B:K.105 Water bridges: B:E.24

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: R.182, R.185, Y.224 10 PLIP interactions: 10 interactions with chain A Water bridges: A:E.177, A:E.177, A:Y.178, A:R.182, A:R.182, A:R.182, A:R.185, A:Y.224 Salt bridges: A:R.182, A:R.185 SO4.6: 4 residues within 4Å: Chain A: R.68, Y.130, A.316, E.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.130, A:E.317 Salt bridges: A:R.68 SO4.7: 4 residues within 4Å: Chain A: R.58, R.61, R.139, R.163 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.61 Water bridges: A:R.139, A:R.139, A:R.139, A:V.179, A:V.179 Salt bridges: A:R.58, A:R.139, A:R.163 SO4.8: 4 residues within 4Å: Chain A: V.5, R.6, S.20, Y.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.21 Salt bridges: A:R.6 SO4.14: 3 residues within 4Å: Chain B: R.182, R.185, Y.224 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.178, B:R.182, B:R.182, B:R.182, B:R.185, B:Y.224, A:H.223 Salt bridges: B:R.182, B:R.185 SO4.15: 4 residues within 4Å: Chain B: R.68, Y.130, A.316, E.317 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.317 Salt bridges: B:R.68 SO4.16: 4 residues within 4Å: Chain B: R.58, R.61, R.139, R.163 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.61, B:Y.196 Water bridges: B:R.139, B:R.139, B:R.139, B:V.179, B:V.179 Salt bridges: B:R.58, B:R.139, B:R.163 SO4.17: 4 residues within 4Å: Chain B: V.5, R.6, S.20, Y.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.21 Salt bridges: B:R.6

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

CL.9: 7 residues within 4Å: Chain A: H.223, Y.224, L.225 Chain B: H.223, Y.224, L.225 Ligands: CL.18 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain A: H.223, Y.224, L.225 Chain B: H.223, Y.224, L.225 Ligands: CL.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Crystal Structure of the ERK2 complexed with 5-Iodotubercidin. To Be Published

Release Date

2024-05-29

Peptides

Mitogen-activated protein kinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Mitogen-activated protein kinase 1

Related Entries With Identical Sequence