SMTL ID : 5x6c.1

Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-4-4-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 15 residues within 4Å: Chain A: R.232, E.234, S.240, H.241, L.242, Y.245, K.285, E.310, V.311, A.312, T.313, G.337, R.340 Chain E: D.157, D.159 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:L.242, A:L.242, A:Y.245, A:V.311, A:T.313, A:T.313, A:G.337, A:R.340, A:R.340, E:D.157, E:D.159 Salt bridges: A:R.232, A:R.232, A:H.241, A:H.241, A:K.285, A:K.285 pi-Stacking: A:Y.245, A:Y.245 ATP.3: 15 residues within 4Å: Chain B: R.232, E.234, S.240, H.241, L.242, Y.245, K.285, E.310, V.311, A.312, T.313, G.337, R.340 Chain F: D.157, D.159 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:E.234, B:E.234, B:E.234, B:L.242, B:E.310, B:E.310, B:T.313, B:T.313, B:G.337, B:R.340, B:R.340, F:D.157, F:D.157 Salt bridges: B:R.232, B:R.232, B:H.241, B:H.241, B:K.285, B:K.285, B:K.285 pi-Stacking: B:Y.245, B:Y.245 ATP.5: 15 residues within 4Å: Chain A: D.157, D.159 Chain E: R.232, E.234, S.240, H.241, L.242, Y.245, K.285, E.310, V.311, A.312, T.313, G.337, R.340 19 PLIP interactions: 2 interactions with chain A, 17 interactions with chain E Hydrogen bonds: A:D.157, A:D.159, E:L.242, E:L.242, E:Y.245, E:V.311, E:T.313, E:T.313, E:G.337, E:R.340, E:R.340 Salt bridges: E:R.232, E:R.232, E:H.241, E:H.241, E:K.285, E:K.285 pi-Stacking: E:Y.245, E:Y.245 ATP.7: 15 residues within 4Å: Chain B: D.157, D.159 Chain F: R.232, E.234, S.240, H.241, L.242, Y.245, K.285, E.310, V.311, A.312, T.313, G.337, R.340 22 PLIP interactions: 20 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:E.234, F:E.234, F:E.234, F:L.242, F:E.310, F:E.310, F:T.313, F:T.313, F:G.337, F:R.340, F:R.340, B:D.157, B:D.157 Salt bridges: F:R.232, F:R.232, F:H.241, F:H.241, F:K.285, F:K.285, F:K.285 pi-Stacking: F:Y.245, F:Y.245

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: H.202, M.203, T.204, S.247, S.249, N.333, L.334, G.335 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.203, A:T.204, A:T.204, A:S.247, A:S.249, A:S.249, A:N.333 SO4.4: 8 residues within 4Å: Chain B: H.202, M.203, T.204, S.247, S.249, N.333, L.334, G.335 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.203, B:T.204, B:T.204, B:S.247, B:S.249, B:N.333 SO4.6: 8 residues within 4Å: Chain E: H.202, M.203, T.204, S.247, S.249, N.333, L.334, G.335 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:M.203, E:T.204, E:T.204, E:S.247, E:S.249, E:S.249, E:N.333 SO4.8: 8 residues within 4Å: Chain F: H.202, M.203, T.204, S.247, S.249, N.333, L.334, G.335 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:M.203, F:T.204, F:T.204, F:S.247, F:S.249, F:N.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, M. et al., Structural basis for tRNA-dependent cysteine biosynthesis. Nat Commun (2017)

Release Date

2017-12-06

Peptides

O-phosphoserine--tRNA(Cys) ligase: ABEF
Uncharacterized protein MJ1481: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
E

D
F

G
E

H
F

O-phosphoserine--tRNA(Cys) ligase

Uncharacterized protein MJ1481

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