SMTL ID : 8dht.1 (1 other biounit)

Crystal structure of a typeIII Rubisco

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 9 residues within 4Å: Chain A: K.160, K.162, K.186, D.188, E.189, H.278 Chain B: N.108 Ligands: 3PG.2, 3PG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.188, A:E.189 MG.8: 8 residues within 4Å: Chain A: N.108 Chain B: K.160, K.186, D.188, E.189, H.278 Ligands: 3PG.9, 3PG.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.188, B:E.189

4 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.2: 11 residues within 4Å: Chain A: K.186, E.189, H.278, R.279, H.311, L.320, S.364, G.365 Chain B: N.108 Ligands: MG.1, 3PG.3 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.364, A:S.364, A:Q.386, B:N.108 Water bridges: A:R.279, A:R.279, A:R.279, A:R.279, A:H.282, A:G.313, A:S.364 Salt bridges: A:H.278, A:R.279, A:H.311, A:H.311 3PG.3: 18 residues within 4Å: Chain A: V.158, K.160, K.162, K.186, D.188, E.189, K.319, G.365, G.366, Q.386, G.388, G.389 Chain B: E.46, T.51, W.52, N.108 Ligands: MG.1, 3PG.2 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.160, A:E.189, A:G.366, A:Q.386, A:G.388, A:G.389, B:T.51, B:N.108 Water bridges: A:K.319, A:G.365, A:L.367, A:L.367, A:G.390, B:T.51 Salt bridges: A:K.160, A:K.160, A:K.162, A:K.319, A:K.319 3PG.9: 12 residues within 4Å: Chain A: N.108 Chain B: K.186, E.189, H.278, R.279, H.311, L.320, S.364, G.365, Q.386 Ligands: MG.8, 3PG.10 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.364, B:S.364, B:Q.386, A:N.108 Water bridges: B:R.279, B:R.279, B:R.279, B:R.279, B:H.282, B:G.313, B:S.364 Salt bridges: B:H.278, B:R.279, B:H.311, B:H.311 3PG.10: 17 residues within 4Å: Chain A: E.46, T.51, W.52, N.108 Chain B: K.160, K.162, K.186, D.188, E.189, K.319, G.365, G.366, Q.386, G.388, G.389 Ligands: MG.8, 3PG.9 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.160, B:E.189, B:G.366, B:Q.386, B:G.388, B:G.389, A:T.51, A:N.108 Water bridges: B:K.319, B:G.365, B:G.365, B:L.367, B:G.390, A:T.51 Salt bridges: B:K.160, B:K.160, B:K.162, B:K.319, B:K.319

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: T.35, I.36, D.76, G.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.36 Water bridges: A:D.76, A:D.76, A:G.80, A:G.80 GOL.5: 4 residues within 4Å: Chain A: R.232, Y.263 Chain B: R.232, Y.263 No protein-ligand interaction detected (PLIP)

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

ACT.6: 3 residues within 4Å: Chain A: N.246, Y.271, D.272 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.272 ACT.7: 4 residues within 4Å: Chain A: E.200, E.233, R.236, R.237 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.237, A:R.237 Salt bridges: A:R.237 ACT.11: 4 residues within 4Å: Chain B: L.125, Q.351, N.352, H.354 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.352 Water bridges: B:Q.124, B:Q.124, B:Q.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Q. et al., Crystal structure of a type III Rubisco in complex with its product 3-phosphoglycerate. Proteins (2023)

Release Date

2022-11-30

Peptides

Ribulose bisphosphate carboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Ribulose bisphosphate carboxylase

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