SMTL ID : 4mkv.1

Structure of Pisum sativum Rubisco with ABA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-8-8-mer

Ligands

8 x RUB: RIBULOSE-1,5-DIPHOSPHATE(Non-covalent)

RUB.1: 18 residues within 4Å: Chain A: K.164, K.166, D.192, E.193, H.283, R.284, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 Chain J: T.54, W.55, N.112 28 PLIP interactions: 25 interactions with chain A, 3 interactions with chain J Hydrogen bonds: A:K.164, A:K.164, A:E.193, A:H.287, A:S.368, A:S.368, A:G.370, A:G.392, A:G.393, J:T.54, J:T.54, J:N.112 Water bridges: A:T.162, A:T.162, A:K.166, A:H.283, A:H.283, A:H.283, A:R.284, A:R.284, A:G.369, A:I.371, A:I.371, A:I.371 Salt bridges: A:K.164, A:R.284, A:H.316, A:K.323 RUB.3: 19 residues within 4Å: Chain B: K.164, K.166, D.192, E.193, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 Chain I: T.54, W.55, N.112 24 PLIP interactions: 21 interactions with chain B, 3 interactions with chain I Hydrogen bonds: B:K.164, B:K.164, B:D.192, B:H.287, B:S.368, B:G.369, B:G.370, B:G.392, B:G.393, I:T.54, I:T.54, I:N.112 Water bridges: B:R.284, B:R.284, B:G.318, B:K.323, B:I.371, B:I.371, B:Q.390, B:G.394 Salt bridges: B:K.164, B:R.284, B:H.316, B:K.323 RUB.5: 18 residues within 4Å: Chain C: K.164, D.192, E.193, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 Chain L: T.54, W.55, N.112 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain L Hydrogen bonds: C:K.164, C:K.164, C:D.192, C:H.287, C:S.368, C:S.368, C:G.370, C:G.392, C:G.393, L:T.54, L:T.54, L:N.112 Water bridges: C:H.283, C:R.284, C:R.284, C:G.318, C:K.323, C:S.368, C:I.371, C:Q.390, C:G.394 Salt bridges: C:K.164, C:R.284, C:H.316, C:K.323 RUB.7: 18 residues within 4Å: Chain D: K.164, D.192, E.193, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 Chain K: T.54, W.55, N.112 23 PLIP interactions: 20 interactions with chain D, 3 interactions with chain K Hydrogen bonds: D:K.164, D:K.164, D:D.192, D:K.323, D:S.368, D:S.368, D:G.370, D:G.392, D:G.393, K:T.54, K:T.54, K:N.112 Water bridges: D:R.284, D:R.284, D:H.287, D:H.287, D:G.369, D:G.394 Salt bridges: D:K.164, D:R.284, D:H.287, D:H.316, D:K.323 RUB.9: 18 residues within 4Å: Chain B: T.54, W.55, N.112 Chain I: K.164, K.166, D.192, E.193, H.283, R.284, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 25 PLIP interactions: 22 interactions with chain I, 3 interactions with chain B Hydrogen bonds: I:K.164, I:K.164, I:E.193, I:H.287, I:H.316, I:S.368, I:S.368, I:G.370, I:G.392, I:G.393, B:T.54, B:N.112 Water bridges: I:T.162, I:R.284, I:R.284, I:S.368, I:G.369, I:I.371, I:I.371, I:I.371, B:T.54 Salt bridges: I:K.164, I:R.284, I:H.316, I:K.323 RUB.11: 19 residues within 4Å: Chain A: T.54, W.55, N.112 Chain J: K.164, K.166, D.192, E.193, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 23 PLIP interactions: 20 interactions with chain J, 3 interactions with chain A Hydrogen bonds: J:K.164, J:K.164, J:D.192, J:H.287, J:S.368, J:G.369, J:G.370, J:G.392, J:G.393, A:T.54, A:N.112 Water bridges: J:R.284, J:R.284, J:G.318, J:I.371, J:I.371, J:Q.390, J:G.394, A:T.54 Salt bridges: J:K.164, J:R.284, J:H.316, J:K.323 RUB.13: 18 residues within 4Å: Chain D: T.54, W.55, N.112 Chain K: K.164, D.192, E.193, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 24 PLIP interactions: 21 interactions with chain K, 3 interactions with chain D Hydrogen bonds: K:K.164, K:K.164, K:D.192, K:H.287, K:H.316, K:S.368, K:S.368, K:G.370, K:G.392, K:G.393, D:T.54, D:N.112 Water bridges: K:R.284, K:R.284, K:G.318, K:S.368, K:I.371, K:Q.390, K:G.394, D:T.54 Salt bridges: K:K.164, K:R.284, K:H.316, K:K.323 RUB.15: 18 residues within 4Å: Chain C: T.54, W.55, N.112 Chain L: K.164, D.192, E.193, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, F.391, G.392, G.393 25 PLIP interactions: 21 interactions with chain L, 4 interactions with chain C Hydrogen bonds: L:K.164, L:K.164, L:D.192, L:H.316, L:K.323, L:S.368, L:S.368, L:G.370, L:G.392, L:G.393, C:T.54, C:N.112 Water bridges: L:R.284, L:R.284, L:H.287, L:H.287, L:G.369, L:G.394, C:T.54, C:T.54 Salt bridges: L:K.164, L:R.284, L:H.287, L:H.316, L:K.323

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

PO4.2: 3 residues within 4Å: Chain A: R.128, F.353, T.354 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.354, A:T.354, A:T.354 Water bridges: A:R.128, A:R.128, A:R.128 PO4.6: 4 residues within 4Å: Chain C: K.345, Y.352, F.353, T.354 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.354, C:T.354 Water bridges: C:R.128 PO4.8: 3 residues within 4Å: Chain D: Y.352, F.353, T.354 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.354, D:T.354 Water bridges: D:R.128, D:T.354 PO4.10: 3 residues within 4Å: Chain I: R.128, F.353, T.354 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:T.354, I:T.354, I:T.354, I:T.354 Water bridges: I:R.128, I:R.128, I:R.128 PO4.14: 4 residues within 4Å: Chain K: K.345, Y.352, F.353, T.354 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:T.354, K:T.354, K:T.354 Water bridges: K:R.128 PO4.16: 3 residues within 4Å: Chain L: Y.352, F.353, T.354 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:T.354, L:T.354, L:T.354 Water bridges: L:R.128

2 x A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid(Non-covalent)

A8S.4: 10 residues within 4Å: Chain B: T.20, L.26, Y.74, E.75, Y.89, R.128, K.345, Y.352, F.353, T.354 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.89, B:Y.89, B:K.345, B:K.345, B:F.353 Hydrogen bonds: B:Y.74 Water bridges: B:R.128, B:R.128, B:R.128 Salt bridges: B:R.128 A8S.12: 10 residues within 4Å: Chain J: T.20, L.26, Y.74, E.75, Y.89, R.128, K.345, Y.352, F.353, T.354 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:Y.89, J:Y.89, J:K.345, J:K.345, J:F.353 Water bridges: J:R.128, J:R.128, J:R.128 Salt bridges: J:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galka, M.M. et al., Identification of Interactions between Abscisic Acid and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase. Plos One (2015)

Release Date

2013-10-16

Peptides

Ribulose bisphosphate carboxylase large chain: ABCDIJKL
Ribulose bisphosphate carboxylase small chain 3A, chloroplastic: EFGHMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

I
A

J
B

K
C

L
D

E
S

F
T

G
U

H
V

M
S

N
T

O
U

P
V

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain 3A, chloroplastic