SMTL ID : 7ct9.1

Crystal structure of SAH bound CmoB from Vibrio Vulnificus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 17 residues within 4Å: Chain A: K.92, K.111, G.131, G.133, H.137, I.152, D.153, P.154, F.158, G.181, I.182, E.183, M.197, G.198, V.199, R.203 Ligands: MLI.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.133, A:I.182, A:E.183, A:M.197 Water bridges: A:K.92, A:K.111, A:H.137, A:H.137, A:R.203 Salt bridges: A:K.92, A:K.111, A:H.137 SAH.4: 17 residues within 4Å: Chain B: K.92, K.111, G.131, G.133, H.137, I.152, D.153, P.154, F.158, G.181, I.182, E.183, M.197, G.198, V.199, R.203 Ligands: MLI.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.133, B:I.182, B:E.183, B:M.197 Water bridges: B:K.92, B:K.111, B:R.203 Salt bridges: B:K.92, B:K.111, B:H.137 SAH.7: 17 residues within 4Å: Chain C: K.92, K.111, G.131, G.133, H.137, I.152, D.153, P.154, F.158, G.181, I.182, E.183, M.197, G.198, V.199, R.203 Ligands: MLI.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.133, C:I.182, C:E.183, C:M.197 Water bridges: C:K.92, C:K.111, C:R.203 Salt bridges: C:K.92, C:K.111, C:H.137 SAH.10: 17 residues within 4Å: Chain D: K.92, K.111, G.131, G.133, H.137, I.152, D.153, P.154, F.158, G.181, I.182, E.183, M.197, G.198, V.199, R.203 Ligands: MLI.11 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.133, D:I.182, D:E.183, D:M.197 Water bridges: D:K.92, D:K.111, D:H.137, D:R.203 Salt bridges: D:K.92, D:K.111, D:H.137

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 8 residues within 4Å: Chain A: K.92, W.106, Y.201, H.202, M.247, R.316 Ligands: SAH.1, PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.106 Salt bridges: A:K.92, A:K.111, A:H.202, A:R.316 MLI.5: 8 residues within 4Å: Chain B: K.92, W.106, G.198, Y.201, H.202, R.316 Ligands: SAH.4, PO4.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.201, B:Y.201, B:Y.201 Water bridges: B:Q.284 Salt bridges: B:K.92, B:K.111, B:H.202, B:R.316 MLI.8: 8 residues within 4Å: Chain C: K.92, W.106, Y.201, H.202, M.247, R.316 Ligands: SAH.7, PO4.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:W.106, C:Y.201 Salt bridges: C:K.92, C:K.111, C:H.202, C:R.316 MLI.11: 8 residues within 4Å: Chain D: K.92, W.106, G.198, Y.201, H.202, R.316 Ligands: SAH.10, PO4.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Y.201, D:Y.201, D:Y.201 Water bridges: D:Q.284 Salt bridges: D:K.92, D:K.111, D:H.202, D:R.316

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: W.106, A.245, M.247, Q.284, Y.298, P.314 Ligands: MLI.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.245, A:Q.284 PO4.6: 7 residues within 4Å: Chain B: W.106, L.228, A.245, Q.284, P.314, R.316 Ligands: MLI.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.245, B:Q.284, B:R.316 PO4.9: 7 residues within 4Å: Chain C: W.106, A.245, M.247, Q.284, Y.298, P.314 Ligands: MLI.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.245, C:Q.284 PO4.12: 7 residues within 4Å: Chain D: W.106, L.228, A.245, Q.284, P.314, R.316 Ligands: MLI.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.245, D:Q.284, D:R.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeong, S. et al., Structural snapshots of CmoB in various states during wobble uridine modification of tRNA. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-03-03

Peptides

tRNA U34 carboxymethyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

tRNA U34 carboxymethyltransferase

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