SMTL ID : 5eul.1

Structure of the SecA-SecY complex with a translocating polypeptide substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.207 Ligands: ADP.3 No protein-ligand interaction detected (PLIP)

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

BEF.2: 4 residues within 4Å: Chain A: T.102, G.103, D.492 Ligands: ADP.3 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.3: 16 residues within 4Å: Chain A: M.79, F.80, P.81, F.82, Q.85, G.103, E.104, G.105, K.106, T.107, L.108, D.492, R.528, Q.529 Ligands: MG.1, BEF.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:F.80, A:Q.85, A:G.103, A:E.104, A:G.105, A:T.107, A:D.492, A:R.528, A:Q.529 Salt bridges: A:K.106

18 x TBR: HEXATANTALUM DODECABROMIDE(Non-covalent)

TBR.4: 8 residues within 4Å: Chain A: D.591, Q.595, Q.598, Y.599, L.740, R.741 Chain B: E.103, R.106 No protein-ligand interaction detected (PLIP) TBR.5: 5 residues within 4Å: Chain A: E.798, M.801, E.802 Chain B: H.255, P.257 No protein-ligand interaction detected (PLIP) TBR.6: 10 residues within 4Å: Chain A: T.251, D.253, T.256, V.298, A.299, M.300, Q.301, E.544, R.547, R.548 No protein-ligand interaction detected (PLIP) TBR.7: 6 residues within 4Å: Chain A: K.302, D.303, E.440, E.443, K.447, K.462 No protein-ligand interaction detected (PLIP) TBR.8: 3 residues within 4Å: Chain A: H.43, E.47, E.50 No protein-ligand interaction detected (PLIP) TBR.9: 5 residues within 4Å: Chain A: N.117, T.120, H.202, E.365, K.366 No protein-ligand interaction detected (PLIP) TBR.10: 6 residues within 4Å: Chain A: E.625, E.628, N.629, K.632, M.689, I.693 No protein-ligand interaction detected (PLIP) TBR.11: 4 residues within 4Å: Chain A: K.723, D.726, H.809, S.813 No protein-ligand interaction detected (PLIP) TBR.12: 11 residues within 4Å: Chain A: Q.770, E.772, D.773, E.778, E.780 Chain B: S.283, G.286, R.295, R.296, F.298, D.299 No protein-ligand interaction detected (PLIP) TBR.13: 7 residues within 4Å: Chain A: K.229, K.232, Y.234, A.285, H.288, H.289, E.348 No protein-ligand interaction detected (PLIP) TBR.14: 6 residues within 4Å: Chain A: E.309, D.310, K.325, K.462, H.464, E.465 No protein-ligand interaction detected (PLIP) TBR.15: 6 residues within 4Å: Chain A: E.443, S.446, K.447, K.450, H.456, V.458 No protein-ligand interaction detected (PLIP) TBR.16: 4 residues within 4Å: Chain A: E.34, E.71, R.74, R.75 No protein-ligand interaction detected (PLIP) TBR.17: 9 residues within 4Å: Chain A: T.376, E.377, E.379, K.583, E.586, G.587, F.590 Chain B: M.104, R.107 No protein-ligand interaction detected (PLIP) TBR.18: 4 residues within 4Å: Chain A: R.14, E.378, E.379, Q.388 No protein-ligand interaction detected (PLIP) TBR.19: 4 residues within 4Å: Chain A: V.281 Chain B: K.234, P.236, P.342 No protein-ligand interaction detected (PLIP) TBR.20: 2 residues within 4Å: Chain A: F.804 Chain B: E.411 No protein-ligand interaction detected (PLIP) TBR.21: 4 residues within 4Å: Chain A: R.553 Chain B: P.93, K.94, E.97 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Crystal structure of a substrate-engaged SecY protein-translocation channel. Nature (2016)

Release Date

2016-03-09

Peptides

Protein translocase subunit SecA, Insertion Peptide Chimera: A
Protein translocase subunit SecY: B
Preprotein translocase SecE subunit: C
AYC08: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
Y

C
E

D
V

Membrane

We predict this structure to be a membrane protein.
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Protein translocase subunit SecA, Insertion Peptide Chimera

Protein translocase subunit SecY

Preprotein translocase SecE subunit

AYC08

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