SMTL ID : 6pxu.1 (1 other biounit)

Crystal structure of human GalNAc-T12 bound to a diglycosylated peptide, Mn2+, and UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-mer

Ligands

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 17 residues within 4Å: Chain A: A.105, F.106, Y.107, D.138, R.167, G.169, L.170, D.190, C.191, H.192, V.296, W.297, H.325, Y.333, R.335 Chain B: T.14 Ligands: MN.10 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.333 Hydrogen bonds: A:Y.107, A:D.138, A:R.167, A:G.169, A:L.170, A:C.191, B:T.14 Water bridges: A:R.335, A:R.335 Salt bridges: A:H.192, A:H.325, A:R.335, A:R.335

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

EDO.2: 5 residues within 4Å: Chain A: E.256, R.259, R.268, W.309, T.393 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.256, A:R.268 EDO.3: 3 residues within 4Å: Chain A: R.142, E.143, H.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.143, A:H.144, A:H.144 EDO.4: 4 residues within 4Å: Chain A: D.223, W.224, N.225 Chain B: R.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.16 EDO.8: 3 residues within 4Å: Chain A: D.71, W.111, R.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.148, A:R.148 EDO.9: 5 residues within 4Å: Chain A: L.175, A.178, S.179, E.285, S.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.175, A:E.285, A:E.285

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.352, F.353, P.401, E.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.401 GOL.6: 7 residues within 4Å: Chain A: R.206, E.256, R.259, Q.261, V.266, R.268, E.316 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.206, A:E.256, A:R.259, A:Q.261, A:R.268 GOL.7: 4 residues within 4Å: Chain A: R.363, L.366, E.367, P.368 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.363, A:L.366

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.10: 4 residues within 4Å: Chain A: D.190, H.192, H.325 Ligands: UDP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:H.192, A:H.325, H2O.1 MN.11: 1 residues within 4Å: Chain A: V.159 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.159, H2O.2, H2O.3

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.12: 10 residues within 4Å: Chain A: I.219, D.220, V.221, L.230, N.232, P.236, Q.237 Chain B: T.17, G.18, A.21 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.221, A:L.230 Hydrogen bonds: A:V.221, A:L.230, A:Q.237, B:T.17 Water bridges: A:N.232 A2G.13: 11 residues within 4Å: Chain A: D.422, N.424, Y.439, H.442, M.444, G.445, Q.446, N.447, Q.448 Chain B: T.5, G.6 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.444 Hydrogen bonds: A:D.422, A:N.424, A:H.442, A:N.447, A:Q.448, B:T.5 Water bridges: A:N.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, A.J. et al., The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-09-25

Peptides

Polypeptide N-acetylgalactosaminyltransferase 12: A
GAGATGAGAGYYITPRTGAGA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Polypeptide N-acetylgalactosaminyltransferase 12

GAGATGAGAGYYITPRTGAGA

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