SMTL ID : 6pxu.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.190, H.192, H.325 Ligands: UDP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:H.192, A:H.325, H2O.5 MN.15: 3 residues within 4Å: Chain A: Y.107, N.108, D.141 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.107, A:D.141, H2O.5

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

UDP.2: 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.1 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.107, A:D.138, A:D.138, A:R.167, A:G.169, A:L.170, A:C.191, A:Y.333, 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

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

EDO.3: 6 residues within 4Å: Chain A: N.232, E.235, Q.237 Chain B: G.18, A.19 Ligands: A2G.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.232, A:Q.237 EDO.4: 6 residues within 4Å: Chain A: E.295, K.337, A.340, P.368, F.369, G.370 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.337, A:F.369 Water bridges: A:E.295, A:G.370 EDO.5: 5 residues within 4Å: Chain A: H.399, R.459, C.483, E.484, E.485 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.459, A:R.459 EDO.11: 3 residues within 4Å: Chain A: D.71, W.111, R.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.148, A:R.148 Water bridges: A:D.71, A:W.111, A:W.111, A:S.112 EDO.12: 3 residues within 4Å: Chain A: Y.139, S.140, D.141 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: D.93, N.96, Q.205, H.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.93, A:N.96, A:Q.205 EDO.14: 3 residues within 4Å: Chain A: D.141, R.142, E.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.141, A:E.143

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: R.206, E.256, R.259, M.260, D.265, V.266, R.268, E.316 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.206, A:R.259, A:R.259, A:R.268, A:E.316, A:E.316 GOL.7: 5 residues within 4Å: Chain A: R.45, Q.56, E.57, V.60, N.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.45, A:Q.56, A:N.225 GOL.8: 3 residues within 4Å: Chain A: L.161, I.162, R.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.163 GOL.9: 3 residues within 4Å: Chain A: H.442, M.444, M.542 No protein-ligand interaction detected (PLIP) GOL.10: 7 residues within 4Å: Chain A: R.255, E.256, R.259, R.268, W.309, T.393, V.394 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.255, A:R.255, A:E.256, A:R.259, A:R.268, A:T.393

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

A2G.16: 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 Ligands: EDO.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.230 Hydrogen bonds: A:D.220, A:V.221, A:L.230, A:N.232, A:Q.237, A:Q.237, B:T.17 Water bridges: A:N.232 A2G.17: 10 residues within 4Å: Chain A: D.422, N.424, Y.439, H.442, 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:Q.446, A:N.447 Hydrogen bonds: A:D.422, 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
B

B
D

Polypeptide N-acetylgalactosaminyltransferase 12

GAGATGAGAGYYITPRTGAGA

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