SMTL ID : 6h4c.1

A polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-12-12-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.117 Chain C: D.117 Chain E: D.117 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:D.117, A:D.117, C:D.117, E:D.117, H2O.1 MG.12: 3 residues within 4Å: Chain G: D.117 Chain I: D.117 Chain K: D.117 5 PLIP interactions: 1 interactions with chain I, 2 interactions with chain G, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: I:D.117, G:D.117, G:D.117, K:D.117, H2O.7 MG.23: 3 residues within 4Å: Chain M: D.117 Chain O: D.117 Chain Q: D.117 5 PLIP interactions: 1 interactions with chain O, 1 interactions with chain Q, 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: O:D.117, Q:D.117, M:D.117, M:D.117, H2O.13 MG.34: 5 residues within 4Å: Chain S: D.117 Chain U: D.117 Chain W: D.117 Ligands: MG.37, MG.40 5 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: U:D.117, W:D.117, S:D.117, H2O.20, H2O.22 MG.37: 5 residues within 4Å: Chain S: D.117 Chain U: D.117 Chain W: D.117 Ligands: MG.34, MG.40 5 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: U:D.117, W:D.117, S:D.117, H2O.19, H2O.22 MG.40: 5 residues within 4Å: Chain S: D.117 Chain U: D.117 Chain W: D.117 Ligands: MG.34, MG.37 5 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: U:D.117, W:D.117, S:D.117, H2O.19, H2O.20

15 x NI: NICKEL (II) ION(Non-functional Binders)(Non-covalent)

NI.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.7: 1 residues within 4Å: Chain C: R.143 No protein-ligand interaction detected (PLIP) NI.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.18: 1 residues within 4Å: Chain I: R.143 No protein-ligand interaction detected (PLIP) NI.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.29: 1 residues within 4Å: Chain O: R.143 No protein-ligand interaction detected (PLIP) NI.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NI.36: 1 residues within 4Å: Chain T: D.96 No protein-ligand interaction detected (PLIP) NI.39: 1 residues within 4Å: Chain V: D.96 No protein-ligand interaction detected (PLIP) NI.42: 1 residues within 4Å: Chain X: D.96 No protein-ligand interaction detected (PLIP)

21 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 10 residues within 4Å: Chain C: S.85, S.90, T.93, H.94, L.95, V.96, I.97 Chain E: K.64, E.98, K.115 Ligand excluded by PLIP PEG.5: 1 residues within 4Å: Chain C: H.94 Ligand excluded by PLIP PEG.6: 2 residues within 4Å: Chain C: H.43 Chain D: N.108 Ligand excluded by PLIP PEG.8: 4 residues within 4Å: Chain D: M.26, G.67, F.92, D.96 Ligand excluded by PLIP PEG.9: 7 residues within 4Å: Chain A: K.64, E.98, K.115 Chain E: S.90, T.93, L.95, V.96 Ligand excluded by PLIP PEG.10: 4 residues within 4Å: Chain A: K.64 Chain E: S.91, K.92, H.94 Ligand excluded by PLIP PEG.15: 10 residues within 4Å: Chain I: S.85, S.90, T.93, H.94, L.95, V.96, I.97 Chain K: K.64, E.98, K.115 Ligand excluded by PLIP PEG.16: 1 residues within 4Å: Chain I: H.94 Ligand excluded by PLIP PEG.17: 2 residues within 4Å: Chain I: H.43 Chain J: N.108 Ligand excluded by PLIP PEG.19: 4 residues within 4Å: Chain J: M.26, G.67, F.92, D.96 Ligand excluded by PLIP PEG.20: 7 residues within 4Å: Chain G: K.64, E.98, K.115 Chain K: S.90, T.93, L.95, V.96 Ligand excluded by PLIP PEG.21: 4 residues within 4Å: Chain G: K.64 Chain K: S.91, K.92, H.94 Ligand excluded by PLIP PEG.26: 10 residues within 4Å: Chain O: S.85, S.90, T.93, H.94, L.95, V.96, I.97 Chain Q: K.64, E.98, K.115 Ligand excluded by PLIP PEG.27: 1 residues within 4Å: Chain O: H.94 Ligand excluded by PLIP PEG.28: 2 residues within 4Å: Chain O: H.43 Chain P: N.108 Ligand excluded by PLIP PEG.30: 4 residues within 4Å: Chain P: M.26, G.67, F.92, D.96 Ligand excluded by PLIP PEG.31: 7 residues within 4Å: Chain M: K.64, E.98, K.115 Chain Q: S.90, T.93, L.95, V.96 Ligand excluded by PLIP PEG.32: 4 residues within 4Å: Chain M: K.64 Chain Q: S.91, K.92, H.94 Ligand excluded by PLIP PEG.35: 6 residues within 4Å: Chain S: F.52, G.153, D.154 Chain T: R.75, Y.117, D.121 Ligand excluded by PLIP PEG.38: 6 residues within 4Å: Chain U: F.52, G.153, D.154 Chain V: R.75, Y.117, D.121 Ligand excluded by PLIP PEG.41: 6 residues within 4Å: Chain W: F.52, G.153, D.154 Chain X: R.75, Y.117, D.121 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rafael Ciges-Tomas, J. et al., The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature. Nat Commun (2019)

Release Date

2019-08-28

Peptides

dUTPase: ACEGIKMOQSUW
Orf20: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
A

I
C

K
E

M
A

O
C

Q
E

S
G

U
G

W
G

B
B

D
D

F
F

H
B

J
D

L
F

N
B

P
D

R
F

T
H

V
H

X
H

dUTPase

Orf20

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