SMTL ID : 3aml.1

Structure of the Starch Branching Enzyme I (BEI) from Oryza sativa L

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 7 residues within 4Å: Chain A: R.421, L.422, A.423, N.453, R.454, C.460 Ligands: SIN.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.453 BME.8: 3 residues within 4Å: Chain A: D.36, C.39, L.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.36

32 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: E.185, M.222, Y.235, R.342, E.399, L.422, M.424, Y.463, S.466, H.467, L.523 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: R.174, R.330, M.333, D.334, L.390 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: D.492, L.493, P.495, R.563 Ligands: GOL.9 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: N.384, H.388, P.410, V.411, D.412, G.417 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain A: D.492, R.563, Y.566, L.642, G.645, G.646, H.647 Ligands: GOL.5, GOL.10 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: Y.566, L.642, V.643 Ligands: GOL.9, GOL.15 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: K.94, E.96, S.104 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: G.622, Y.623, K.624, F.671 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: R.182, R.212, N.215, Y.216, N.217, G.264, E.579 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: D.560, K.565, A.569, V.643 Ligands: GOL.10, GOL.32 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: F.146, G.152, A.153, Y.155, S.228, R.246 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: R.454, R.455, Y.456, T.457 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: E.84, F.85, P.117, S.120 Ligand excluded by PLIP GOL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain A: L.577, E.580, F.581, A.636, Y.691 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain A: S.555, L.556, T.559, H.561, L.562 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain A: W.160, P.250, E.251, K.254, Y.331, E.335 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: K.57, F.58, R.70, I.102, R.323 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain A: Y.34, M.381, V.411, G.414 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain A: W.72, P.74, F.100, H.294, E.295 Ligands: EPE.3 Ligand excluded by PLIP GOL.26: 10 residues within 4Å: Chain A: H.187, G.189, Y.200, A.223, I.224, H.227, Y.230, S.244, R.246, S.247 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain A: R.649, V.650, G.651, V.654, L.681 Ligands: SIN.34 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain A: W.88, N.89, R.125 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain A: P.630, P.675, N.676 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain A: P.74, A.75, Q.77, K.97, E.295 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain A: K.177, P.178, D.179, A.180, P.181, F.420, K.459 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain A: K.565, N.568, A.569, Q.572 Ligands: GOL.15 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain A: D.439, R.502, P.616, R.685 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain A: D.98, K.99 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain A: P.495, A.496, S.497 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain A: S.228, Y.229, W.545 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain A: E.580, F.581 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 7 residues within 4Å: Chain A: L.40, H.44, F.100, W.319, E.320, R.323 Ligands: GOL.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.320, A:E.320

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

ACT.6: 3 residues within 4Å: Chain A: G.473, D.474, K.475 No protein-ligand interaction detected (PLIP)

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.11: 7 residues within 4Å: Chain A: D.400, V.401, G.403, R.421, R.454, R.455 Ligands: BME.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.403, A:G.403, A:R.455 Water bridges: A:A.425, A:R.455 Salt bridges: A:R.421 SIN.34: 7 residues within 4Å: Chain A: G.622, V.654, D.655, K.679, V.680, L.681 Ligands: GOL.27 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.622, A:K.679, A:K.679 Water bridges: A:D.655, A:K.679 Salt bridges: A:H.656

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noguchi, J. et al., Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding. Glycobiology (2011)

Release Date

2011-09-28

Peptides

Os06g0726400 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Os06g0726400 protein