SMTL ID : 6iwr.2 (2 other biounits)

Crystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.241, H.243, H.380 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.241, A:H.243 MN.4: 5 residues within 4Å: Chain B: D.241, H.243, H.380 Ligands: NAG.2, UDP.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.241, B:H.243, B:H.380

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 15 residues within 4Å: Chain B: L.220, R.224, D.241, I.270, A.328, G.329, G.330, W.352, G.353, G.354, E.355, N.356, H.380 Ligands: UDP.3, MN.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.224, B:G.330, B:G.353, B:E.355, B:E.355

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

UDP.3: 17 residues within 4Å: Chain B: V.154, F.155, H.156, E.158, D.187, R.217, G.219, L.220, R.224, D.241, A.242, H.243, W.352, H.380, R.383 Ligands: NAG.2, MN.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.220 Hydrogen bonds: B:H.156, B:E.158, B:D.187, B:R.217, B:L.220, B:A.242 Salt bridges: B:H.243, B:H.380, B:R.383

1 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.5: 13 residues within 4Å: Chain A: K.103, Q.107 Chain B: G.397, S.398, S.399, D.487, M.489, H.503, M.505, G.506, G.507, N.508, Q.509 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:M.505 Hydrogen bonds: B:G.397, B:D.487, B:M.489, B:H.503, B:H.503, B:N.508, B:Q.509, A:Q.107 Salt bridges: A:K.103, A:K.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, C. et al., Structural basis of carbohydrate transfer activity of UDP-GalNAc: Polypeptide N-acetylgalactosaminyltransferase 7. Biochem. Biophys. Res. Commun. (2019)

Release Date

2019-02-06

Peptides

N-acetylgalactosaminyltransferase 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

N-acetylgalactosaminyltransferase 7

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