SMTL ID : 5znm.1

Colicin D Central Domain and C-terminal tRNase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: K.300 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.300 SO4.2: 6 residues within 4Å: Chain A: P.220, T.221, H.226 Chain B: S.131, Q.133, E.275 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.221, A:T.221, B:S.131, B:S.131 Water bridges: A:N.225, B:A.276, B:A.276, B:A.276 Salt bridges: A:H.226 SO4.3: 4 residues within 4Å: Chain A: Q.294, K.297, K.298, L.366 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.294 Salt bridges: A:K.297, A:K.298 SO4.12: 4 residues within 4Å: Chain B: K.298, K.300, H.301, S.367 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.339, B:S.367 Salt bridges: B:K.298, B:K.300, B:H.301 SO4.13: 4 residues within 4Å: Chain B: Q.294, K.297, K.298, L.366 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.294 Salt bridges: B:K.297, B:K.298 SO4.14: 5 residues within 4Å: Chain A: Q.133, E.275 Chain B: P.220, T.221, H.226 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Water bridges: A:E.275, A:E.275, A:A.276, A:A.276, B:N.225, B:N.225 Hydrogen bonds: B:T.221, B:T.221 Salt bridges: B:H.226

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.326, H.327, D.330, N.350 Ligands: GOL.5, GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.326, A:D.330, A:D.330 Water bridges: A:H.327, A:N.350 GOL.5: 2 residues within 4Å: Chain A: E.326 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.6: 1 residues within 4Å: Chain A: E.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.383 Water bridges: A:R.379 GOL.7: 2 residues within 4Å: Chain A: T.353 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.8: 2 residues within 4Å: Chain A: L.183, N.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.184 Water bridges: A:N.184, A:T.197 GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.10: 9 residues within 4Å: Chain A: G.23, V.24, N.25, N.52, D.194, V.211, P.213, Y.264, W.265 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.25, A:N.25, A:R.187, A:W.265 Water bridges: A:N.25 GOL.11: 5 residues within 4Å: Chain A: D.188, T.191, L.193, K.195, L.210 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.191, A:T.191 Water bridges: A:D.188, A:K.195, A:K.195 GOL.15: 10 residues within 4Å: Chain B: V.24, N.25, N.52, A.185, R.187, D.194, V.211, Y.264, W.265, R.266 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.25, B:N.25, B:N.52, B:R.187, B:W.265 Water bridges: B:N.25 GOL.16: 7 residues within 4Å: Chain A: A.7, E.10, A.11 Chain B: Y.30, T.31, Q.227, P.228 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.30, B:Q.227, A:E.10 Water bridges: B:Y.30, B:Q.32 GOL.17: 4 residues within 4Å: Chain B: E.326, H.327, D.330, N.350 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.326, B:E.326, B:E.326, B:D.330 Water bridges: B:N.350 GOL.18: 6 residues within 4Å: Chain B: K.21, G.145, A.146, T.147, V.182, N.184 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.20, B:V.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, J.W. et al., Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell. J. Biochem. (2018)

Release Date

2018-08-29

Peptides

Colicin-D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Colicin-D