SMTL ID : 5hql.1

Structure function studies of R. palustris RubisCO (A47V-M331A mutant; CABP-bound; no expression tag)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-hexamer

Ligands

6 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Non-covalent)

CAP.1: 23 residues within 4Å: Chain A: I.165, K.167, K.169, K.192, D.194, E.195, H.288, R.289, H.292, H.322, G.324, K.330, S.369, G.370, G.371, M.372, A.393, G.394, G.395 Chain B: E.49, T.54, N.112 Ligands: MG.2 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.167, A:H.288, A:G.371, A:G.394, A:G.395, B:T.54, B:T.54, B:N.112 Water bridges: A:R.289, A:H.292, A:S.369, A:M.372 Salt bridges: A:K.167, A:K.167, A:K.169, A:R.289, A:H.322, A:K.330, A:K.330 CAP.3: 23 residues within 4Å: Chain A: E.49, T.54, N.112 Chain B: I.165, K.167, K.169, K.192, D.194, E.195, H.288, R.289, H.292, H.322, G.324, K.330, S.369, G.370, G.371, A.393, G.394, G.395, G.396 Ligands: MG.4 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.167, B:E.195, B:H.288, B:H.292, B:S.369, B:S.369, B:G.371, B:G.394, B:G.395, A:T.54, A:N.112 Water bridges: B:K.169, B:R.289, B:R.289, B:M.372, B:M.372, B:G.396, B:G.396 Salt bridges: B:K.167, B:K.167, B:K.169, B:R.289, B:H.322, B:K.330, B:K.330 CAP.5: 22 residues within 4Å: Chain C: I.165, K.167, K.169, K.192, D.194, E.195, H.288, R.289, H.292, H.322, G.324, K.330, S.369, G.370, G.371, A.393, G.394, G.395 Chain E: E.49, T.54, N.112 Ligands: MG.6 23 PLIP interactions: 20 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:K.167, C:E.195, C:H.288, C:H.292, C:S.369, C:S.369, C:G.371, C:G.394, C:G.395, E:T.54, E:T.54, E:N.112 Water bridges: C:G.370, C:M.372, C:G.396, C:G.396 Salt bridges: C:K.167, C:K.167, C:K.169, C:R.289, C:H.322, C:K.330, C:K.330 CAP.7: 23 residues within 4Å: Chain D: I.165, K.167, K.169, K.192, D.194, E.195, H.288, R.289, H.292, H.322, G.324, K.330, S.369, G.370, G.371, M.372, A.393, G.394, G.395 Chain F: E.49, T.54, N.112 Ligands: MG.8 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:K.167, D:E.195, D:E.195, D:H.288, D:H.292, D:S.369, D:G.371, D:G.394, D:G.395, F:T.54, F:T.54, F:N.112 Water bridges: D:S.369, D:M.372 Salt bridges: D:K.167, D:K.167, D:K.169, D:R.289, D:H.322, D:K.330, D:K.330 CAP.9: 24 residues within 4Å: Chain C: E.49, T.54, N.112 Chain E: I.165, K.167, K.169, K.192, D.194, E.195, H.288, R.289, H.292, H.322, G.324, K.330, S.369, G.370, G.371, M.372, A.393, G.394, G.395, G.396 Ligands: MG.10 21 PLIP interactions: 18 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:K.167, E:E.195, E:H.288, E:S.369, E:G.371, E:G.394, E:G.395, C:T.54, C:N.112 Water bridges: E:K.169, E:R.289, E:G.370, E:M.372, C:E.49 Salt bridges: E:K.167, E:K.167, E:K.169, E:R.289, E:H.322, E:K.330, E:K.330 CAP.11: 25 residues within 4Å: Chain D: E.49, T.54, N.112 Chain F: I.165, K.167, K.169, K.192, D.194, E.195, H.288, R.289, H.292, H.322, G.324, K.330, A.331, S.369, G.370, G.371, M.372, A.393, G.394, G.395, G.396 Ligands: MG.12 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:K.167, F:D.194, F:H.288, F:S.369, F:G.371, F:G.394, F:G.395, D:T.54, D:T.54, D:N.112 Water bridges: F:S.369, F:G.370 Salt bridges: F:K.167, F:K.167, F:K.169, F:R.289, F:H.292, F:H.322, F:K.330, F:K.330

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 9 residues within 4Å: Chain A: I.165, K.167, K.169, K.192, D.194, E.195, H.288 Chain B: N.112 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.194, A:E.195 MG.4: 9 residues within 4Å: Chain A: N.112 Chain B: I.165, K.167, K.169, K.192, D.194, E.195, H.288 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.194, B:E.195 MG.6: 9 residues within 4Å: Chain C: I.165, K.167, K.169, K.192, D.194, E.195, H.288 Chain E: N.112 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.194, C:E.195 MG.8: 9 residues within 4Å: Chain D: I.165, K.167, K.169, K.192, D.194, E.195, H.288 Chain F: N.112 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.194, D:E.195 MG.10: 9 residues within 4Å: Chain C: N.112 Chain E: I.165, K.167, K.169, K.192, D.194, E.195, H.288 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.194, E:E.195 MG.12: 9 residues within 4Å: Chain D: N.112 Chain F: I.165, K.167, K.169, K.192, D.194, E.195, H.288 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.194, F:E.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arbing, M.A. et al., Structure function studies of R. palustris RubisCO. To Be Published

Release Date

2017-01-25

Peptides

Ribulose bisphosphate carboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Ribulose bisphosphate carboxylase