SMTL ID : 6huf.1 (3 other biounits)

Coping with strong translational non-crystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.23, T.41, D.64 Ligands: GNP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.23, A:T.41, H2O.1 MG.3: 4 residues within 4Å: Chain B: T.23, T.41, D.64 Ligands: GNP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.23, B:T.41 MG.5: 5 residues within 4Å: Chain C: T.23, T.41, D.64, T.65 Ligands: GNP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.23, C:T.41 MG.7: 4 residues within 4Å: Chain D: T.23, T.41, D.64 Ligands: GNP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.23, D:T.41

4 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 23 residues within 4Å: Chain A: D.17, S.18, G.19, V.20, G.21, K.22, T.23, S.24, F.34, S.36, F.38, T.40, T.41, T.65, G.67, N.123, K.124, D.126, L.127, S.153, A.154, A.155 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.19, A:G.21, A:K.22, A:K.22, A:T.23, A:T.23, A:S.24, A:S.24, A:S.36, A:T.41, A:T.41, A:G.67, A:N.123, A:K.124, A:A.154, A:A.155 Salt bridges: A:D.126 pi-Stacking: A:F.34 GNP.4: 23 residues within 4Å: Chain B: D.17, S.18, G.19, V.20, G.21, K.22, T.23, S.24, F.34, S.36, F.38, T.40, T.41, T.65, G.67, N.123, K.124, D.126, L.127, S.153, A.154, A.155 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:D.17, B:G.19, B:V.20, B:G.21, B:K.22, B:K.22, B:T.23, B:T.23, B:S.24, B:S.24, B:S.36, B:T.41, B:T.65, B:G.67, B:N.123, B:K.124, B:A.154, B:A.155 Salt bridges: B:D.126 pi-Stacking: B:F.34 GNP.6: 23 residues within 4Å: Chain C: D.17, S.18, G.19, V.20, G.21, K.22, T.23, S.24, F.34, S.36, F.38, T.40, T.41, T.65, G.67, N.123, K.124, D.126, L.127, S.153, A.154, A.155 Ligands: MG.5 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:D.17, C:G.19, C:V.20, C:G.21, C:K.22, C:K.22, C:T.23, C:S.24, C:S.24, C:S.36, C:T.41, C:T.41, C:T.65, C:G.67, C:N.123, C:K.124, C:A.154, C:A.155 Salt bridges: C:D.126 pi-Stacking: C:F.34 GNP.8: 23 residues within 4Å: Chain D: D.17, S.18, G.19, V.20, G.21, K.22, T.23, S.24, F.34, S.36, F.38, T.40, T.41, T.65, G.67, N.123, K.124, D.126, L.127, S.153, A.154, A.155 Ligands: MG.7 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.19, D:G.21, D:K.22, D:K.22, D:T.23, D:S.24, D:S.24, D:S.36, D:T.41, D:T.41, D:T.65, D:G.67, D:N.123, D:K.124, D:A.154, D:A.155 Salt bridges: D:D.126 pi-Stacking: D:F.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamshidiha, M. et al., Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-03-27

Peptides

Ras-related protein Rab-27A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ras-related protein Rab-27A

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