SMTL ID : 2znd.1

Crystal structure of Ca2+-free form of des3-20ALG-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

10 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 8 residues within 4Å: Chain A: R.47, I.50, S.51, D.54, N.57, K.58, A.59, G.60 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.50, A:D.54 Hydrogen bonds: A:D.54, A:D.54, A:N.57, A:A.59 MRD.2: 6 residues within 4Å: Chain A: S.34, N.35, G.36, Q.77, R.81, F.129 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.81 Hydrogen bonds: A:S.34, A:R.81 Water bridges: A:S.34 MRD.3: 5 residues within 4Å: Chain A: T.143, F.146, D.150, G.155 Chain B: Y.161 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.146, A:D.150 Hydrogen bonds: A:D.150, A:G.155 MRD.4: 5 residues within 4Å: Chain A: Y.72, D.75, W.76, V.79 Ligands: MRD.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.72, A:D.75, A:W.76, A:W.76, A:V.79 Water bridges: A:Q.140 MRD.5: 6 residues within 4Å: Chain A: F.103, G.104, Y.105, Q.140, R.147 Ligands: MRD.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.105, A:Q.140 Water bridges: A:Y.105 MRD.11: 8 residues within 4Å: Chain B: R.47, I.50, S.51, D.54, N.57, K.58, A.59, G.60 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.50, B:D.54 Hydrogen bonds: B:D.54, B:D.54, B:N.57, B:A.59 MRD.12: 6 residues within 4Å: Chain B: S.34, N.35, G.36, Q.77, R.81, F.129 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.81 Hydrogen bonds: B:S.34, B:R.81 Water bridges: B:S.34 MRD.13: 5 residues within 4Å: Chain A: Y.161 Chain B: T.143, F.146, D.150, G.155 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.146, B:D.150 Hydrogen bonds: B:D.150, B:G.155 MRD.14: 5 residues within 4Å: Chain B: Y.72, D.75, W.76, V.79 Ligands: MRD.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.72, B:D.75, B:W.76, B:W.76, B:V.79 Water bridges: B:Q.140 MRD.15: 6 residues within 4Å: Chain B: F.103, G.104, Y.105, Q.140, R.147 Ligands: MRD.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.105, B:Q.140 Water bridges: B:Y.105

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 3 residues within 4Å: Chain A: T.39, R.121, Q.122 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.121, A:R.121, A:R.121 Salt bridges: A:R.121 PO4.7: 3 residues within 4Å: Chain A: F.119 Chain B: F.169, V.172 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.118, A:K.118 Salt bridges: A:K.118 PO4.16: 3 residues within 4Å: Chain B: T.39, R.121, Q.122 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.121, B:R.121, B:R.121 Salt bridges: B:R.121 PO4.17: 3 residues within 4Å: Chain A: F.169, V.172 Chain B: F.119 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.118, B:K.118 Salt bridges: B:K.118

6 x NA: SODIUM ION(Non-functional Binders)

NA.8: 6 residues within 4Å: Chain A: D.17, D.19, S.21, V.23, I.24, E.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.19, A:S.21 Water bridges: A:S.21, A:S.21 NA.9: 5 residues within 4Å: Chain A: D.84, D.86, S.88, M.90, E.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88, A:E.95 Water bridges: A:D.86 NA.10: 4 residues within 4Å: Chain A: D.150, D.152, D.154, W.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.152, A:D.154, A:W.156 NA.18: 6 residues within 4Å: Chain B: D.17, D.19, S.21, V.23, I.24, E.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.17, B:D.19 Water bridges: B:S.21, B:S.21 NA.19: 5 residues within 4Å: Chain B: D.84, D.86, S.88, M.90, E.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.88, B:S.88 Water bridges: B:D.86 NA.20: 4 residues within 4Å: Chain B: D.150, D.152, D.154, W.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.154, B:W.156, B:W.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, H. et al., Structural Basis for Ca(2+)-Dependent Formation of ALG-2/Alix Peptide Complex: Ca(2+)/EF3-Driven Arginine Switch Mechanism. Structure (2008)

Release Date

2008-09-09

Peptides

Programmed cell death protein 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Programmed cell death protein 6

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