SMTL ID : 2wq8.1

Glycan labelling using engineered variants of galactose oxidase obtained by directed evolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x CU: COPPER (II) ION(Non-covalent)

CU.1: 7 residues within 4Å: Chain A: F.249, C.250, Y.294, Y.517, H.518, H.603 Ligands: ACY.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:Y.294, A:Y.517, A:H.518, A:H.603

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: K.51, D.54, N.56, T.59, A.163, E.164 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:K.51, A:N.56, A:T.59, A:T.59, A:A.163

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 7 residues within 4Å: Chain A: F.216, Y.294, F.312, F.486, Y.517, H.518 Ligands: CU.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.216 Hydrogen bonds: A:Y.517 Salt bridges: A:K.352, A:H.518 ACY.4: 11 residues within 4Å: Chain A: W.358, R.393, A.400, A.403, T.420, F.421, G.422, N.435, A.436, H.437 Ligands: EDO.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.358, A:A.403, A:N.435 Hydrogen bonds: A:T.420, A:T.420, A:H.437 Salt bridges: A:R.393, A:H.437

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 9 residues within 4Å: Chain A: A.400, P.401, D.402, A.403, G.422, G.423, T.433, N.435 Ligands: ACY.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.393, A:P.401, A:G.422, A:T.433 EDO.6: 9 residues within 4Å: Chain A: N.407, A.408, V.409, T.465, S.466, T.604, N.606, Q.609 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.408, A:S.466 Water bridges: A:A.408, A:N.606 EDO.7: 10 residues within 4Å: Chain A: T.465, S.519, I.520, S.521, A.601, T.602, H.603, T.604, V.605 Ligands: EDO.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.521, A:S.521, A:T.602, A:T.604 Water bridges: A:S.519, A:H.603 EDO.8: 7 residues within 4Å: Chain A: I.497, Q.508, F.550, P.552, N.553, Y.554 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.508, A:N.553, A:Y.554 EDO.9: 9 residues within 4Å: Chain A: P.94, W.103, I.104, W.127, F.128, A.129, D.130, K.134, A.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.134 Water bridges: A:I.104 EDO.10: 6 residues within 4Å: Chain A: H.356, A.357, W.358, G.406, T.604, V.605 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.357, A:G.406 EDO.11: 4 residues within 4Å: Chain A: L.180, Y.458, Y.506, K.507 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.458, A:K.507 EDO.12: 8 residues within 4Å: Chain A: P.178, G.179, L.180, G.181, R.182, N.553, Y.556, G.560 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.179, A:G.181, A:R.182, A:N.553 EDO.13: 5 residues within 4Å: Chain A: P.613, L.614, T.615, Q.627, P.629 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.613, A:T.615 Water bridges: A:Q.627

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 8 residues within 4Å: Chain A: V.290, F.317, E.318, K.319, N.320, G.321, S.333, P.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.318, A:N.320, A:N.320 GOL.15: 5 residues within 4Å: Chain A: H.62, Y.65, R.95, N.99, N.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.95, A:R.95, A:N.101 Water bridges: A:Y.65 GOL.16: 5 residues within 4Å: Chain A: V.499, Y.506, Q.508, N.553 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.508, A:N.553

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rannes, J.B. et al., Glycoprotein Labeling Using Engineered Variants of Galactose Oxidase Obtained by Directed Evolution. J.Am.Chem.Soc. (2011)

Release Date

2010-09-01

Peptides

GALACTOSE OXIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GALACTOSE OXIDASE