SMTL ID : 5lxx.1

High-resolution structure of human collapsin response mediator protein 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: M.94, T.95, Q.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.95, A:Q.351 SO4.2: 2 residues within 4Å: Chain A: R.135, Y.479 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.135, A:R.135, A:H.170 Salt bridges: A:R.135 SO4.3: 3 residues within 4Å: Chain A: H.300, S.303, K.308 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.304, A:K.308, A:K.308, A:K.308 Salt bridges: A:H.300, A:K.308 SO4.4: 3 residues within 4Å: Chain A: R.411 Chain B: R.411, A.413 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Water bridges: B:N.37, B:R.411, A:Q.40, A:Q.40, A:R.411, A:R.411, A:R.411 Salt bridges: B:R.411, A:R.411 SO4.6: 3 residues within 4Å: Chain B: H.300, S.303, K.308 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.303 Water bridges: B:S.303, B:K.304, B:K.308, B:K.308, B:K.308 Salt bridges: B:H.300, B:K.308 SO4.8: 3 residues within 4Å: Chain C: M.94, T.95, Q.351 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.95, C:Q.351 SO4.9: 2 residues within 4Å: Chain C: R.135, Y.479 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.135, C:R.135, C:H.170 Salt bridges: C:R.135 SO4.10: 3 residues within 4Å: Chain C: H.300, S.303, K.308 6 PLIP interactions: 6 interactions with chain C Water bridges: C:K.304, C:K.308, C:K.308, C:K.308 Salt bridges: C:H.300, C:K.308 SO4.11: 3 residues within 4Å: Chain C: R.411 Chain D: R.411, A.413 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Water bridges: C:Q.40, C:Q.40, C:R.411, C:R.411, C:R.411, D:N.37, D:R.411 Salt bridges: C:R.411, D:R.411 SO4.13: 3 residues within 4Å: Chain D: H.300, S.303, K.308 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.303 Water bridges: D:S.303, D:K.304, D:K.308, D:K.308, D:K.308 Salt bridges: D:H.300, D:K.308

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.5: 12 residues within 4Å: Chain A: R.86, M.89, P.90, D.91, V.120, Y.178, F.181, R.184, F.185, K.265, C.345, E.364 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:P.90, A:Y.178, A:R.184, A:R.184, A:E.364 Water bridges: A:R.86, A:R.86, A:Q.92, A:K.265, A:K.265, A:E.364, A:E.364 Salt bridges: A:D.91 BTB.7: 12 residues within 4Å: Chain B: R.86, M.89, P.90, D.91, V.120, Y.178, F.181, R.184, F.185, K.265, C.345, E.364 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:P.90, B:R.184, B:R.184, B:E.364 Water bridges: B:R.86, B:R.86, B:D.91, B:Q.92, B:K.265, B:K.265, B:S.315, B:E.364 Salt bridges: B:D.91 BTB.12: 12 residues within 4Å: Chain C: R.86, M.89, P.90, D.91, V.120, Y.178, F.181, R.184, F.185, K.265, C.345, E.364 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:P.90, C:Y.178, C:R.184, C:R.184, C:E.364, C:E.364 Water bridges: C:R.86, C:R.86, C:D.91, C:Q.92, C:K.265, C:K.265, C:E.364, C:E.364 Salt bridges: C:D.91 BTB.14: 12 residues within 4Å: Chain D: R.86, M.89, P.90, D.91, V.120, Y.178, F.181, R.184, F.185, K.265, C.345, E.364 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:P.90, D:R.184, D:R.184, D:E.364, D:E.364 Water bridges: D:R.86, D:R.86, D:Q.92, D:K.265, D:K.265, D:S.315, D:E.364 Salt bridges: D:D.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Myllykoski, M. et al., Collapsin response mediator protein 2: high-resolution crystal structure sheds light on small-molecule binding, post-translational modifications, and conformational flexibility. Amino Acids (2017)

Release Date

2017-01-11

Peptides

Dihydropyrimidinase-related protein 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydropyrimidinase-related protein 2

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