SMTL ID : 5jcz.1 (2 other biounits)

Rab11 bound to MyoVa-GTD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.27, T.45 Ligands: GDP.2, BEF.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.27, A:T.45, H2O.1, H2O.1

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 21 residues within 4Å: Chain A: D.21, S.22, G.23, V.24, G.25, K.26, S.27, N.28, F.38, N.39, L.40, S.42, N.126, K.127, D.129, L.130, S.156, A.157, L.158 Ligands: MG.1, BEF.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.23, A:V.24, A:G.25, A:K.26, A:S.27, A:N.28, A:N.28, A:N.39, A:S.42, A:K.43, A:N.126, A:K.127, A:K.127, A:A.157, A:L.158 Water bridges: A:L.40, A:S.42, A:T.45, A:T.45 Salt bridges: A:K.26, A:D.129 pi-Stacking: A:F.38

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 9 residues within 4Å: Chain A: S.22, G.23, K.26, S.44, T.45, A.70, G.71 Ligands: MG.1, GDP.2 No protein-ligand interaction detected (PLIP)

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

EDO.4: 10 residues within 4Å: Chain A: L.18, I.19, G.20, T.69, A.70, G.71, R.74, Y.82, W.107, E.110 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.20, A:G.20, A:R.74, A:R.74, A:E.110 EDO.5: 2 residues within 4Å: Chain A: R.131, R.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.131, A:R.134 EDO.6: 5 residues within 4Å: Chain A: Y.101, E.102, V.104, E.105, F.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.104, A:E.105, A:E.105 EDO.9: 9 residues within 4Å: Chain B: Y.236, G.239, A.240, L.243, T.285, L.286, P.288, L.289, M.361 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.286, B:L.289 EDO.10: 4 residues within 4Å: Chain A: R.35 Chain B: E.269, E.270, R.273 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.35 Hydrogen bonds: B:R.273

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: R.142, F.152, I.153, E.154, N.162 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.154, A:N.162 Water bridges: A:R.142, A:R.142 Salt bridges: A:R.142

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: Y.12, L.13, F.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.13 Water bridges: A:D.11 GOL.11: 7 residues within 4Å: Chain A: E.49 Chain B: R.262, E.269, K.283, E.287, I.290, Q.294 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.262, B:E.269, B:K.283, B:K.283, A:E.49 Water bridges: B:Q.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pylypenko, O. et al., Coordinated recruitment of Spir actin nucleators and myosin V motors to Rab11 vesicle membranes. Elife (2016)

Release Date

2016-09-28

Peptides

Ras-related protein Rab-11A: A
Unconventional myosin-Va: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ras-related protein Rab-11A

Unconventional myosin-Va

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