SMTL ID : 4yxm.1

Structure of Thermotoga maritima DisA D75N mutant with reaction product c-di-AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-octamer

Ligands

4 x 2BA: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide(Non-covalent)

2BA.1: 21 residues within 4Å: Chain A: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131 Chain B: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131, R.148 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:N.95, A:N.95, A:N.95, A:G.96, A:L.114, A:L.114, A:T.127, A:T.131, B:N.95, B:N.95, B:G.96, B:L.114, B:L.114, B:T.127, B:T.127, B:R.148 Water bridges: A:R.128, A:R.128, A:R.128, A:R.128, B:R.128 2BA.3: 21 residues within 4Å: Chain C: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131 Chain D: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131, R.148 21 PLIP interactions: 9 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:N.95, D:N.95, D:G.96, D:L.114, D:L.114, D:T.127, D:T.127, D:R.148, C:N.95, C:N.95, C:N.95, C:G.96, C:L.114, C:L.114, C:T.127, C:T.131 Water bridges: D:R.128, C:R.128, C:R.128, C:R.128, C:R.128 2BA.5: 21 residues within 4Å: Chain E: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131 Chain F: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131, R.148 21 PLIP interactions: 12 interactions with chain E, 9 interactions with chain F Hydrogen bonds: E:N.95, E:N.95, E:N.95, E:G.96, E:L.114, E:L.114, E:T.127, E:T.131, F:N.95, F:N.95, F:G.96, F:L.114, F:L.114, F:T.127, F:T.127, F:R.148 Water bridges: E:R.128, E:R.128, E:R.128, E:R.128, F:R.128 2BA.7: 21 residues within 4Å: Chain G: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131 Chain H: L.59, N.95, G.96, A.97, V.112, H.113, L.114, T.127, R.128, T.131, R.148 21 PLIP interactions: 12 interactions with chain G, 9 interactions with chain H Hydrogen bonds: G:N.95, G:N.95, G:N.95, G:G.96, G:L.114, G:L.114, G:T.127, G:T.131, H:N.95, H:N.95, H:G.96, H:L.114, H:L.114, H:T.127, H:T.127, H:R.148 Water bridges: G:R.128, G:R.128, G:R.128, G:R.128, H:R.128

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

MPD.2: 10 residues within 4Å: Chain A: Q.74, G.75, N.95, N.111, V.112, H.113 Chain B: E.124, T.125, G.126, R.130 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.95 Hydrogen bonds: A:Q.74, A:G.76, A:H.113 MPD.4: 10 residues within 4Å: Chain C: Q.74, G.75, N.95, N.111, V.112, H.113 Chain D: E.124, T.125, G.126, R.130 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.95 Hydrogen bonds: C:Q.74, C:G.76, C:H.113 MPD.6: 10 residues within 4Å: Chain E: Q.74, G.75, N.95, N.111, V.112, H.113 Chain F: E.124, T.125, G.126, R.130 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:N.95 Hydrogen bonds: E:Q.74, E:G.76, E:H.113 MPD.8: 10 residues within 4Å: Chain G: Q.74, G.75, N.95, N.111, V.112, H.113 Chain H: E.124, T.125, G.126, R.130 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:N.95 Hydrogen bonds: G:Q.74, G:G.76, G:H.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muller, M. et al., Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3'-dATP. Biochem.J. (2015)

Release Date

2015-06-03

Peptides

DNA integrity scanning protein DisA: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

DNA integrity scanning protein DisA