SMTL ID : 3wrx.1 (1 other biounit)

Crystal structure of helicase complex 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 16 residues within 4Å: Chain A: T.16, D.18, T.19, K.20, S.54, T.55, S.56, R.92, A.95, G.124, S.125, G.126, G.127 Chain B: D.432, R.435, V.436 21 PLIP interactions: 4 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:D.432, B:R.435, A:T.16, A:D.18, A:T.55, A:S.56, A:R.92, A:R.92, A:G.124, A:G.126, A:G.127 Water bridges: B:R.435, B:R.435, A:K.20, A:K.20, A:K.20, A:K.20 Salt bridges: A:K.20, A:K.20, A:R.92, A:R.92 AGS.8: 16 residues within 4Å: Chain B: P.170, G.171, C.172, G.173, K.174, T.175, K.176, R.203, Q.271, L.302, R.303, G.379, T.381, R.411, T.413 Ligands: MG.9 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.171, B:G.173, B:K.174, B:K.174, B:T.175, B:T.175, B:K.176, B:R.303, B:R.303, B:G.379, B:G.379, B:R.411, B:R.411 Water bridges: B:R.203, B:R.203, B:R.203, B:E.242, B:G.379 Salt bridges: B:K.174, B:R.203, B:R.303, B:R.303

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: M.85, G.86 Chain B: N.313, Y.316, G.318 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:N.313, B:Y.316, A:M.85, A:G.86, H2O.15 MG.9: 3 residues within 4Å: Chain B: T.175, D.241 Ligands: AGS.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.175, H2O.11, H2O.13, H2O.13

8 x CS: CESIUM ION(Non-covalent)

CS.3: 4 residues within 4Å: Chain A: T.271, D.275, M.308, N.310 No protein-ligand interaction detected (PLIP) CS.4: 4 residues within 4Å: Chain A: L.397, E.398, N.400, C.403 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.403 CS.5: 3 residues within 4Å: Chain A: S.76, H.78, T.79 No protein-ligand interaction detected (PLIP) CS.6: 4 residues within 4Å: Chain A: S.37, F.38, S.39, N.40 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.39 CS.7: 4 residues within 4Å: Chain A: N.36, S.37, S.39, K.41 No protein-ligand interaction detected (PLIP) CS.10: 3 residues within 4Å: Chain B: L.348, G.350, I.352 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.348, H2O.11 CS.11: 2 residues within 4Å: Chain B: E.12, H.15 No protein-ligand interaction detected (PLIP) CS.12: 2 residues within 4Å: Chain B: S.20, I.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishibashi, K. et al., Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-08-13

Peptides

Tm-1 protein: A
Replicase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Tm-1 protein

Replicase large subunit

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