SMTL ID : 9y4s.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-octamer

Ligands

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

CL.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: R.32 Chain D: H.110 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: D.28 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: I.133 Chain C: D.28 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: S.106, H.110 Chain C: R.32 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain C: I.133 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain F: H.110, S.128, S.130 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain F: H.110 Chain G: R.32 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain G: H.110 Chain H: R.32 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain E: R.32 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 8 residues within 4Å: Chain A: S.106, R.109, H.110, S.128, H.129, S.130 Chain B: R.32 Ligands: 2BA.14 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.109, A:R.109, B:R.32, B:R.32

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 11 residues within 4Å: Chain C: E.105, S.106, R.109, H.110, S.128, H.129, S.130, M.131 Chain D: R.32, T.67 Ligands: 2BA.20 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.105, C:S.106, C:R.109, C:S.128, D:R.32

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.12: 18 residues within 4Å: Chain B: L.41, D.76, G.77, V.93, Q.94, L.95, T.108, R.109, S.112 Chain E: L.41, D.76, G.77, V.93, Q.94, L.95, T.108, R.109, S.112 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain E Hydrogen bonds: B:D.76, B:D.76, B:G.77, B:L.95, B:L.95, B:T.108, B:T.108, B:R.109, B:R.109, B:S.112, E:D.76, E:G.77, E:L.95, E:L.95, E:T.108, E:T.108, E:R.109, E:S.112 2BA.14: 20 residues within 4Å: Chain A: L.41, D.76, G.77, V.93, Q.94, L.95, G.107, 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: PGE.4 19 PLIP interactions: 9 interactions with chain F, 10 interactions with chain A Hydrogen bonds: F:D.76, F:G.77, F:L.95, F:L.95, F:T.108, F:T.108, F:R.109, F:R.109, F:S.112, A:D.76, A:D.76, A:G.77, A:L.95, A:L.95, A:T.108, A:T.108, A:R.109, A:R.109, A:S.112 2BA.17: 18 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 18 PLIP interactions: 10 interactions with chain D, 8 interactions with chain G Hydrogen bonds: D:D.76, D:D.76, D:G.77, D:L.95, D:L.95, D:T.108, D:T.108, D:R.109, D:R.109, D:S.112, G:D.76, G:G.77, G:L.95, G:L.95, G:T.108, G:T.108, G:R.109, G:S.112 2BA.20: 19 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, V.93, Q.94, L.95, T.108, R.109, S.112 Ligands: PG4.8 19 PLIP interactions: 9 interactions with chain C, 10 interactions with chain H Hydrogen bonds: C:D.76, C:D.76, C:G.77, C:L.95, C:L.95, C:T.108, C:T.108, C:R.109, C:S.112, H:D.76, H:D.76, H:G.77, H:L.95, H:L.95, H:T.108, H:T.108, H:R.109, H:S.112 Salt bridges: H:R.109

Links

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Citation

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

Release Date

2025-09-17

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