SMTL ID : 6zga.1

COPII on membranes, inner coat

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

2 x PRO- PRO- PRO: PRO-PRO-PRO(Non-covalent)

PRO-PRO-PRO.1: 4 residues within 4Å: Chain A: M.633, W.672, Y.677, Y.683 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.672, A:Y.677, A:Y.677, A:Y.683 Hydrogen bonds: D:Q.91 PRO-PRO-PRO.2: 3 residues within 4Å: Chain D: M.633, W.672, Y.683 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.672

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.55, C.60, S.62, C.79, C.82 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.55, A:C.60, A:C.79, A:C.82 ZN.4: 6 residues within 4Å: Chain B: C.231, R.233, C.234, S.236, C.253, C.256 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.231, B:C.234, B:C.253, B:C.256 ZN.7: 4 residues within 4Å: Chain D: C.55, C.60, C.79, C.82 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.55, D:C.60, D:C.79, D:C.82 ZN.8: 4 residues within 4Å: Chain E: C.231, C.234, C.253, C.256 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.231, E:C.234, E:C.253, E:C.256

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Covalent)

GNP.5: 18 residues within 4Å: Chain A: R.721 Chain C: L.31, D.32, N.33, A.34, G.35, K.36, T.37, T.38, T.50, P.53, T.54, G.76, N.132, K.133, V.173, V.174 Ligands: MG.6 21 PLIP interactions: 3 interactions with chain A, 18 interactions with chain C Hydrogen bonds: A:R.721, A:R.721, C:N.33, C:A.34, C:G.35, C:K.36, C:K.36, C:K.36, C:T.37, C:T.37, C:T.38, C:T.38, C:T.50, C:T.54, C:N.132, C:N.132, C:K.133, C:V.173, C:V.174 Salt bridges: A:R.721, C:D.135 GNP.9: 19 residues within 4Å: Chain D: R.721 Chain F: L.31, D.32, N.33, A.34, G.35, K.36, T.37, T.38, Q.52, P.53, T.54, N.132, K.133, D.135, S.172, V.173, V.174 Ligands: MG.10 21 PLIP interactions: 18 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:N.33, F:A.34, F:G.35, F:K.36, F:K.36, F:T.37, F:T.37, F:T.37, F:T.38, F:T.38, F:T.38, F:T.54, F:N.132, F:K.133, F:V.173, F:V.174, D:R.721, D:R.721 Salt bridges: F:D.135, D:R.721 pi-Cation interactions: F:K.133

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain C: K.36, T.37 Ligands: GNP.5 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain F: K.36, T.37, D.73 Ligands: GNP.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hutchings, J. et al., Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network. Nat Commun (2021)

Release Date

2021-02-17

Peptides

Protein transport protein SEC23: AD
Protein transport protein SEC24: BE
Small COPII coat GTPase SAR1: C
Small COPII coat GTPase SAR1: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

B
B

E
F

C
C

F
G

Protein transport protein SEC23

Protein transport protein SEC24

Small COPII coat GTPase SAR1

Small COPII coat GTPase SAR1

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