SMTL ID : 7wik.2 (1 other biounit)

Crystal structure of oligoribonuclease of Mycobacterium smegmatis mc2 155

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: Q.62, R.66 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.66 SO4.6: 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 SO4.7: 3 residues within 4Å: Chain A: R.22, D.79, L.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.80 Water bridges: A:R.22, A:R.22, A:A.81 Salt bridges: A:R.22 SO4.8: 2 residues within 4Å: Chain A: P.145, R.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.146 Salt bridges: A:R.146 SO4.11: 3 residues within 4Å: Chain A: R.3, H.127 Chain B: R.141 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Water bridges: A:R.3, A:R.3, A:K.99, B:R.141 Salt bridges: A:R.3, A:H.127, B:R.141 SO4.16: 5 residues within 4Å: Chain A: Y.128, R.129 Chain B: N.106, S.107, S.134 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.106, B:S.107, B:S.134, B:S.134, A:Y.128, A:Y.128 Water bridges: B:K.137 Salt bridges: B:K.137, A:R.129 SO4.17: 3 residues within 4Å: Chain B: R.22, D.79, L.80 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.80 Water bridges: B:R.22, B:R.22, B:D.79, B:A.81 Salt bridges: B:R.22 SO4.18: 2 residues within 4Å: Chain B: P.145, R.146 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:P.183 Hydrogen bonds: B:R.146 Salt bridges: B:R.146

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.10, C.11, E.12, D.163 Ligands: GOL.9 No protein-ligand interaction detected (PLIP) K.13: 4 residues within 4Å: Chain B: D.10, C.11, E.12, D.163 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.12

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

ACT.3: 2 residues within 4Å: Chain A: V.57, D.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.58, A:D.58 ACT.4: 5 residues within 4Å: Chain A: K.137, Y.148, Q.151, K.154 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 Salt bridges: A:K.137, A:K.154, B:R.129 ACT.5: 3 residues within 4Å: Chain A: E.153, E.166, R.169 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.169 ACT.14: 2 residues within 4Å: Chain B: V.57, D.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.58 ACT.15: 4 residues within 4Å: Chain A: R.129 Chain B: K.137, Y.148, Q.151 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.148, B:Q.151 Salt bridges: B:K.137, A:R.129

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: E.12, M.13, G.15, L.16, V.60, M.63, H.64 Ligands: K.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.12, A:M.13 Water bridges: A:E.12 GOL.19: 7 residues within 4Å: Chain B: E.12, M.13, T.14, G.15, L.16, V.60, H.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.12, B:E.12, B:M.13

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: M.63, H.64, S.67, H.158, R.159 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.64, A:S.67, A:H.158

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 6 residues within 4Å: Chain A: L.18, R.117 Chain B: L.18, G.113, A.116, R.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.113

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
C

B
D

Oligoribonuclease

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