SMTL ID : 5box.1

Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: A.77, N.78, E.81, Q.85 Chain C: T.135, K.139, N.160, L.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.78 GOL.3: 4 residues within 4Å: Chain B: F.29, L.32, E.36, V.40 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain B: E.93, E.94, A.97, K.98 Chain D: E.11, H.12 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.94, B:K.98, D:H.12 GOL.7: 9 residues within 4Å: Chain C: L.151, D.153, A.158, L.161, E.162, I.165, L.179, L.187, I.192 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.162, C:E.162 Water bridges: C:L.161 GOL.8: 7 residues within 4Å: Chain B: R.244, A.247, L.248, E.251 Chain C: D.210, K.252, Y.256 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.210, C:K.252, C:K.252, C:Y.256 GOL.9: 8 residues within 4Å: Chain D: L.151, D.153, G.155, A.158, V.159, I.165, L.179, L.183 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.153, D:A.158 Water bridges: D:L.161 GOL.10: 7 residues within 4Å: Chain A: R.244, A.247, E.251 Chain D: D.210, L.211, K.252, Y.256 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.252, D:Y.256

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 9 residues within 4Å: Chain A: F.209, D.210, L.211, K.252, E.255, Y.256 Chain D: R.244, A.247, E.251 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.256 Hydrophobic interactions: D:A.247 MPD.5: 10 residues within 4Å: Chain B: F.209, D.210, L.211, K.252, E.255, Y.256 Chain C: R.244, A.247, L.248, E.251 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.256 Hydrophobic interactions: C:A.247 MPD.6: 10 residues within 4Å: Chain B: N.78, E.81, K.82, Q.85 Chain D: T.135, L.136, K.139, V.159, N.160, L.161 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:T.135, D:N.160, D:L.161 Hydrogen bonds: B:Q.85, B:Q.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, M.U. et al., Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein. J.Mol.Biol. (2015)

Release Date

2015-09-02

Peptides

Putative HTH-type transcriptional regulator TrmBL2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative HTH-type transcriptional regulator TrmBL2

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