SMTL ID : 5mle.1

Crystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: S.130, D.160, R.161, F.162, Q.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.163 PEG.9: 10 residues within 4Å: Chain B: A.157, F.158, K.159, G.190, I.193, Q.197, R.215, T.337, E.341 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.158, B:K.159, B:R.215, B:T.337 PEG.10: 9 residues within 4Å: Chain B: G.28, T.90, D.122, K.386, D.394, D.396, S.436, Q.437, R.455 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.90, B:D.122, B:Q.437, B:R.455

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

EDO.2: 8 residues within 4Å: Chain A: P.55, G.56, R.385, K.386, G.387, R.388, D.394, D.396 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.56, A:R.385, A:G.387, A:R.388 Water bridges: A:D.396 EDO.3: 2 residues within 4Å: Chain A: E.209, W.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.209, A:W.279 EDO.4: 3 residues within 4Å: Chain A: N.232, N.235, G.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.232, A:N.235, A:G.259 EDO.5: 6 residues within 4Å: Chain A: K.285, F.289, Y.419, N.420, I.421, E.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.421, A:E.423 EDO.6: 8 residues within 4Å: Chain A: R.63, F.64, Q.65, M.66, D.94, H.95, V.97, W.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.63, A:W.111 EDO.7: 7 residues within 4Å: Chain A: M.244, S.270, T.273, L.295, S.296, T.301, P.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.270, A:L.295, A:S.296 EDO.11: 3 residues within 4Å: Chain B: S.404, V.405, K.406 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.405, B:K.406 Water bridges: B:D.401 EDO.12: 4 residues within 4Å: Chain B: N.232, N.235, G.259, R.473 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.232, B:R.473 EDO.13: 1 residues within 4Å: Chain B: N.414 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.414, B:N.414 EDO.14: 8 residues within 4Å: Chain B: Q.197, H.211, R.215, F.336, T.337, I.339, E.341 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.211

2 x NI: NICKEL (II) ION(Non-covalent)

NI.8: 6 residues within 4Å: Chain A: V.60, H.61, H.95, H.126, Q.184, E.265 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.60, A:H.95, A:E.265 NI.15: 6 residues within 4Å: Chain B: V.60, H.61, H.95, H.126, Q.184, E.265 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, Y. et al., Tuning microtubule dynamics to enhance cancer therapy by modulating FER-mediated CRMP2 phosphorylation. Nat Commun (2018)

Release Date

2017-02-22

Peptides

Dihydropyrimidinase-related protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

Dihydropyrimidinase-related protein 2