SMTL ID : 6zay.1

Crystal structure of Atg16L in complex with GDP-bound Rab33B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: K.107, L.110, A.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.107 PO4.2: 5 residues within 4Å: Chain A: Q.138, L.148, E.150, N.159, D.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.159, A:D.160 PO4.8: 4 residues within 4Å: Chain B: W.55, E.58 Chain D: W.55, E.58 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:W.55, B:E.58, D:E.58 PO4.9: 4 residues within 4Å: Chain C: K.107, L.110, A.112, N.113 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.110, C:A.112 PO4.10: 5 residues within 4Å: Chain B: E.47 Chain C: R.68 Chain D: N.48, Q.49, V.52 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.49 Salt bridges: C:R.68

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

PEG.3: 7 residues within 4Å: Chain A: N.17, D.89, T.91, N.92, K.123, L.126 Ligands: GDP.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.91, A:N.92, A:K.123 Water bridges: A:N.17, A:D.89 PEG.4: 3 residues within 4Å: Chain A: H.97, L.136, F.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.136 PEG.13: 5 residues within 4Å: Chain C: A.94, H.97, S.98, S.101 Ligands: PEG.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.101, C:S.101 PEG.15: 4 residues within 4Å: Chain C: L.148, E.150, N.159, D.160 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.150, C:N.159 PEG.16: 7 residues within 4Å: Chain C: Y.78, N.80, V.81, H.82, L.110, L.111, I.115 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.78, C:L.111 Water bridges: C:H.82 PEG.17: 4 residues within 4Å: Chain C: S.101, W.102, E.105 Ligands: PEG.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.101, C:S.101, C:E.105

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

EDO.5: 5 residues within 4Å: Chain A: I.103, C.106, K.107, L.110, R.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.117 EDO.11: 5 residues within 4Å: Chain C: I.103, C.106, K.107, L.110, R.117 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.117 EDO.12: 4 residues within 4Å: Chain C: R.26, G.30, K.154, P.156 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.26, C:R.26 Water bridges: C:F.32 EDO.14: 3 residues within 4Å: Chain C: P.100, F.140, H.144 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.144

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: T.21, E.37, T.39 Ligands: GDP.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.21, A:T.39, H2O.1, H2O.1 MG.18: 4 residues within 4Å: Chain C: T.21, E.37, T.39 Ligands: GDP.19 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.21, C:E.37, C:T.39, H2O.4

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

GDP.7: 19 residues within 4Å: Chain A: D.15, S.16, N.17, V.18, G.19, K.20, T.21, C.22, F.32, T.36, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: PEG.3, MG.6 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:D.15, A:N.17, A:V.18, A:G.19, A:K.20, A:T.21, A:T.21, A:C.22, A:T.36, A:N.122, A:K.123, A:K.123, A:S.152, A:A.153, A:K.154 Water bridges: A:S.16, A:K.20, A:K.20, A:K.20, A:T.36, A:T.36, A:T.39, A:T.63 Salt bridges: A:K.20, A:D.125 pi-Stacking: A:F.32, A:F.32 GDP.19: 18 residues within 4Å: Chain C: D.15, S.16, N.17, V.18, G.19, K.20, T.21, C.22, F.32, T.36, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.18 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:D.15, C:N.17, C:V.18, C:G.19, C:K.20, C:T.21, C:T.21, C:C.22, C:T.36, C:N.122, C:K.123, C:K.123, C:S.152, C:A.153, C:K.154 Water bridges: C:S.16, C:N.17, C:N.17, C:K.20 Salt bridges: C:K.20, C:D.125 pi-Stacking: C:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pantoom, S. et al., RAB33B recruits the ATG16L1 complex to the phagophore via a noncanonical RAB binding protein. Autophagy (2021)

Release Date

2020-09-30

Peptides

Ras-related protein Rab-33B: AC
Autophagy-related protein 16-1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

Ras-related protein Rab-33B

Autophagy-related protein 16-1

Related Entries With Identical Sequence