SMTL ID : 6y09.1

Crystal structure of Atg16L in complex with GTP-bound Rab33B (Q92L)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.21, T.39, D.62 Ligands: GTP.2 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.8: 4 residues within 4Å: Chain C: T.21, T.39, D.62 Ligands: GTP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.21, C:T.39

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 22 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, A.38, T.39, G.65, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.1, PEG.4 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:N.17, A:V.18, A:G.19, A:K.20, A:T.21, A:T.21, A:C.22, A:T.39, A:T.39, A:G.65, A:N.122, A:K.123, A:S.152, A:A.153, A:K.154 Water bridges: A:T.21, A:T.21, A:T.36, A:T.36, A:T.36, A:T.36, A:T.36, A:T.39, A:L.66, A:L.66 Salt bridges: A:K.20, A:K.20, A:D.125 pi-Stacking: A:F.32 GTP.9: 22 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, A.38, T.39, A.64, G.65, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.8 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:C.22, C:T.39, C:G.65, C:N.122, C:K.123, C:K.123, C:S.152, C:A.153, C:K.154 Water bridges: C:T.36, C:L.66, C:L.66 Salt bridges: C:K.20, C:K.20, C:D.125 pi-Stacking: C:F.32

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

PO4.3: 5 residues within 4Å: Chain A: K.107, L.110, A.112, N.113 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.110 PO4.7: 4 residues within 4Å: Chain B: W.55, E.58 Chain D: W.55, E.58 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:E.58, D:E.58, B:E.58, B:E.58 PO4.10: 5 residues within 4Å: Chain C: K.107, L.110, A.112, N.113 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.107 Water bridges: C:K.107, C:L.110, C:L.111 PO4.19: 5 residues within 4Å: Chain B: E.47 Chain C: R.68 Chain D: N.48, Q.49, V.52 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Salt bridges: C:R.68 Hydrogen bonds: D:Q.49, B:E.47

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

PEG.4: 6 residues within 4Å: Chain A: D.89, T.91, N.92, K.123, L.126 Ligands: GTP.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.91, A:N.92, A:K.123 Water bridges: A:D.89 PEG.5: 4 residues within 4Å: Chain A: H.97, L.136, K.139, F.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.97, A:L.136 PEG.6: 6 residues within 4Å: Chain A: I.103, C.106, K.107, L.110, R.117 Ligands: PO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.117 Water bridges: A:A.112, A:N.113 PEG.12: 4 residues within 4Å: Chain C: R.26, K.154, N.155, P.156 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.26, C:R.26, C:N.155 Water bridges: C:G.30 PEG.13: 5 residues within 4Å: Chain C: D.15, A.94, H.97, S.98 Ligands: PEG.18 No protein-ligand interaction detected (PLIP) PEG.15: 5 residues within 4Å: Chain C: Q.138, L.148, E.150, N.159, D.160 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.150, C:E.150, C:N.159 PEG.16: 7 residues within 4Å: Chain C: Y.78, N.80, V.81, H.109, L.110, L.111, I.115 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.109, C:L.111 PEG.17: 3 residues within 4Å: Chain C: S.101, W.102, E.105 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.101 Water bridges: C:W.102 PEG.18: 9 residues within 4Å: Chain C: D.15, S.16, N.17, V.18, D.89, N.92, S.95, K.123 Ligands: PEG.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.15, C:N.92 Water bridges: C:N.17, C:N.17, C:K.123

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

EDO.11: 6 residues within 4Å: Chain C: I.103, C.106, K.107, L.110, R.117 Ligands: PO4.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.103, C:R.117 Water bridges: C:A.112, C:N.113 EDO.14: 3 residues within 4Å: Chain C: P.100, F.140, H.144 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.144 Water bridges: C:T.143

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

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