SMTL ID : 9y9y.1

Crystal structure of DNA integrity scanning protein DisA from Mycobacterium tuberculosis in complex with cyclic di-AMP and bromide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 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: 20 residues within 4Å: Chain A: L.41, D.76, G.77, V.93, Q.94, L.95, T.108, R.109, S.112 Chain F: L.41, D.76, G.77, V.93, Q.94, L.95, T.108, R.109, S.112 Ligands: BR.2, BR.11 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain F Hydrogen bonds: A:D.76, A:G.77, A:L.95, A:L.95, A:T.108, A:R.109, A:S.112, F:D.76, F:G.77, F:L.95, F:L.95, F:T.108, F:T.108, F:R.109, F:S.112 2BA.8: 22 residues within 4Å: Chain B: L.41, D.76, G.77, V.93, Q.94, L.95, G.107, T.108, R.109, S.112 Chain E: L.41, D.76, G.77, V.93, Q.94, L.95, G.107, T.108, R.109, S.112 Ligands: BR.3, BR.9 19 PLIP interactions: 9 interactions with chain E, 10 interactions with chain B Hydrogen bonds: E:D.76, E:G.77, E:L.95, E:L.95, E:T.108, E:T.108, E:R.109, E:R.109, E:S.112, B:G.77, B:Q.94, B:L.95, B:L.95, B:T.108, B:T.108, B:R.109, B:R.109, B:S.112 Salt bridges: B:R.109 2BA.12: 20 residues within 4Å: Chain D: L.41, D.76, G.77, V.93, Q.94, L.95, T.108, R.109, S.112 Chain G: L.41, D.76, G.77, V.93, Q.94, L.95, T.108, R.109, S.112 Ligands: BR.7, BR.13 16 PLIP interactions: 8 interactions with chain G, 8 interactions with chain D Hydrogen bonds: G:D.76, G:G.77, G:L.95, G:L.95, G:T.108, G:R.109, G:S.112, D:G.77, D:Q.94, D:L.95, D:L.95, D:T.108, D:T.108, D:R.109, D:S.112 Salt bridges: G:R.109 2BA.14: 21 residues within 4Å: Chain C: L.41, D.76, G.77, V.93, Q.94, L.95, T.108, R.109, S.112 Chain H: L.41, D.76, G.77, A.78, V.93, Q.94, L.95, T.108, R.109, S.112 Ligands: BR.5, BR.15 18 PLIP interactions: 9 interactions with chain H, 9 interactions with chain C Hydrogen bonds: H:D.76, H:A.78, H:Q.94, H:L.95, H:L.95, H:T.108, H:T.108, H:R.109, H:S.112, C:D.76, C:G.77, C:L.95, C:L.95, C:T.108, C:T.108, C:R.109, C:R.109, C:S.112

8 x BR: BROMIDE ION(Non-covalent)

BR.2: 5 residues within 4Å: Chain A: R.109, S.128, H.129, S.130 Ligands: 2BA.1 Ligand excluded by PLIP BR.3: 5 residues within 4Å: Chain B: R.109, S.128, H.129, S.130 Ligands: 2BA.8 Ligand excluded by PLIP BR.5: 5 residues within 4Å: Chain C: R.109, S.128, H.129, S.130 Ligands: 2BA.14 Ligand excluded by PLIP BR.7: 6 residues within 4Å: Chain D: R.109, H.110, S.128, H.129, S.130 Ligands: 2BA.12 Ligand excluded by PLIP BR.9: 6 residues within 4Å: Chain E: R.109, H.110, S.128, H.129, S.130 Ligands: 2BA.8 Ligand excluded by PLIP BR.11: 6 residues within 4Å: Chain F: R.109, H.110, S.128, H.129, S.130 Ligands: 2BA.1 Ligand excluded by PLIP BR.13: 6 residues within 4Å: Chain G: R.109, H.110, S.128, H.129, S.130 Ligands: 2BA.12 Ligand excluded by PLIP BR.15: 5 residues within 4Å: Chain H: R.109, H.110, S.128, H.129 Ligands: 2BA.14 Ligand excluded by PLIP

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain B: D.28 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: V.62, R.63 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain E: V.62, R.63, R.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Crystal structure of DNA integrity scanning protein DisA from Mycobacterium tuberculosis in complex with cyclic di-AMP and bromide. To be published

Release Date

2025-09-24

Peptides

DNA integrity scanning protein DisA: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

DNA integrity scanning protein DisA

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