SMTL ID : 7wik.1 (1 other biounit)

Crystal structure of oligoribonuclease of Mycobacterium smegmatis mc2 155

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: D.10, C.11, E.12, D.163 No protein-ligand interaction detected (PLIP) K.7: 4 residues within 4Å: Chain B: D.10, C.11, E.12, D.163 No protein-ligand interaction detected (PLIP)

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain A: V.57, D.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.58 ACT.3: 4 residues within 4Å: Chain A: K.137, Y.148, Q.151 Chain B: R.129 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.151, A:Q.151 Water bridges: A:Y.148 Salt bridges: A:K.137, B:R.129 ACT.8: 2 residues within 4Å: Chain B: V.57, D.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.58 ACT.9: 3 residues within 4Å: Chain B: R.22, D.79, L.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.80 Water bridges: B:R.22, B:H.47, B:A.81 Salt bridges: B:R.22

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: N.106, S.107, S.134 Chain B: Y.128, R.129 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.106, A:S.107, A:S.134 Water bridges: A:K.137 Salt bridges: A:K.137, B:R.129 SO4.6: 3 residues within 4Å: Chain A: R.141 Chain B: R.3, H.127 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.129, B:R.129 Salt bridges: B:R.3, B:H.127, A:R.141 SO4.10: 3 residues within 4Å: Chain A: R.3, H.127 Chain B: R.141 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.3, A:H.127, B:R.141 Water bridges: B:R.141 SO4.11: 2 residues within 4Å: Chain B: P.145, R.146 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.146 Water bridges: B:P.145, B:R.146, A:P.183 Salt bridges: B:R.146 SO4.13: 4 residues within 4Å: Chain B: K.61, T.70, E.71, R.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.71 Water bridges: B:K.61 Salt bridges: B:K.61, B:R.74

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: E.12, M.13, T.14, G.15, L.16, V.60, H.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.12, A:M.13, A:T.14 GOL.12: 7 residues within 4Å: Chain B: E.12, M.13, T.14, G.15, L.16, V.60, H.64 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.12, B:E.12, B:M.13, B:M.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Badhwar, P. et al., Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer. J.Biol.Chem. (2022)

Release Date

2022-12-21

Peptides

Oligoribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Oligoribonuclease

Related Entries With Identical Sequence