SMTL ID : 9h3f.1

Cryo-EM structure of YhaM

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.195, H.219, H.251, H.252 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.219, A:H.251, A:H.252 MG.2: 5 residues within 4Å: Chain A: H.164, M.168, H.194, D.195, D.275 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.164, A:H.194, A:D.195, A:D.275 MG.3: 4 residues within 4Å: Chain B: D.195, H.219, H.251, H.252 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.195, B:H.219, B:H.251, B:H.252 MG.4: 5 residues within 4Å: Chain B: H.164, M.168, H.194, D.195, D.275 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.164, B:H.194, B:D.195, B:D.275 MG.5: 4 residues within 4Å: Chain C: D.195, H.219, H.251, H.252 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.195, C:H.219, C:H.251, C:H.252 MG.6: 5 residues within 4Å: Chain C: H.164, M.168, H.194, D.195, D.275 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.194, C:D.195, C:D.275 MG.7: 4 residues within 4Å: Chain D: D.195, H.219, H.251, H.252 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.195, D:H.219, D:H.251, D:H.252 MG.8: 5 residues within 4Å: Chain D: H.164, M.168, H.194, D.195, D.275 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.164, D:H.194, D:D.195, D:D.275 MG.9: 4 residues within 4Å: Chain E: D.195, H.219, H.251, H.252 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.219, E:H.251, E:H.252 MG.10: 5 residues within 4Å: Chain E: H.164, M.168, H.194, D.195, D.275 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.164, E:H.194, E:D.195, E:D.275 MG.11: 4 residues within 4Å: Chain F: D.195, H.219, H.251, H.252 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.195, F:H.219, F:H.251, F:H.252 MG.12: 5 residues within 4Å: Chain F: H.164, M.168, H.194, D.195, D.275 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.164, F:H.194, F:D.195, F:D.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanssmann, J. et al., A conserved nuclease facilitates environmental DNA uptake. Nucleic Acids Res. (2025)

Release Date

2025-08-06

Peptides

3'-5' exoribonuclease YhaM: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

3'-5' exoribonuclease YhaM