SMTL ID : 1omz.2 (1 other biounit)

crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) in complex with UDPGalNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

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

MN.1: 2 residues within 4Å: Chain A: D.116 Ligands: UD2.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.116, H2O.1, H2O.1, H2O.5 MN.4: 3 residues within 4Å: Chain B: D.116, N.235 Ligands: UD2.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.116, H2O.6, H2O.6, H2O.6 MN.7: 2 residues within 4Å: Chain C: D.116 Ligands: UD2.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.116, H2O.10, H2O.10, H2O.14 MN.10: 3 residues within 4Å: Chain D: D.116, N.235 Ligands: UD2.11 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.116, H2O.15, H2O.15, H2O.15 MN.13: 2 residues within 4Å: Chain E: D.116 Ligands: UD2.14 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.116, H2O.20, H2O.20, H2O.24 MN.16: 3 residues within 4Å: Chain F: D.116, N.235 Ligands: UD2.17 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.116, H2O.25, H2O.25, H2O.25 MN.19: 2 residues within 4Å: Chain G: D.116 Ligands: UD2.20 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.116, H2O.29, H2O.29, H2O.33 MN.22: 3 residues within 4Å: Chain H: D.116, N.235 Ligands: UD2.23 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.116, H2O.34, H2O.34, H2O.34

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

UD2.2: 20 residues within 4Å: Chain A: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.37 Hydrogen bonds: A:Q.35, A:Y.37, A:N.64, A:N.93, A:N.93, A:R.98, A:R.98, A:D.114, A:D.114, A:D.115, A:D.115, A:G.178, A:Q.205, A:R.256 Water bridges: A:Q.35, A:R.39, A:R.39, A:D.209, A:D.209 Salt bridges: A:R.39, A:H.252, A:H.252, A:R.256 UD2.5: 20 residues within 4Å: Chain B: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.37 Hydrogen bonds: B:Q.35, B:N.64, B:N.93, B:N.93, B:R.98, B:R.98, B:D.114, B:D.114, B:D.114, B:D.115, B:D.115, B:Q.205, B:D.208, B:R.256 Water bridges: B:R.39, B:R.39, B:G.178 Salt bridges: B:R.39, B:H.252, B:H.252, B:R.256 UD2.8: 20 residues within 4Å: Chain C: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.7 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:Y.37 Hydrogen bonds: C:Q.35, C:Y.37, C:N.64, C:N.93, C:N.93, C:R.98, C:R.98, C:D.114, C:D.114, C:D.115, C:D.115, C:G.178, C:Q.205, C:R.256 Water bridges: C:Q.35, C:R.39, C:R.39, C:D.209, C:D.209 Salt bridges: C:R.39, C:H.252, C:H.252, C:R.256 UD2.11: 20 residues within 4Å: Chain D: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.10 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Y.37 Hydrogen bonds: D:Q.35, D:N.64, D:N.93, D:N.93, D:R.98, D:R.98, D:D.114, D:D.114, D:D.114, D:D.115, D:D.115, D:Q.205, D:D.208, D:R.256 Water bridges: D:R.39, D:R.39, D:G.178 Salt bridges: D:R.39, D:H.252, D:H.252, D:R.256 UD2.14: 20 residues within 4Å: Chain E: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.13 24 PLIP interactions: 24 interactions with chain E Hydrophobic interactions: E:Y.37 Hydrogen bonds: E:Q.35, E:Y.37, E:N.64, E:N.93, E:N.93, E:R.98, E:R.98, E:D.114, E:D.114, E:D.115, E:D.115, E:G.178, E:Q.205, E:R.256 Water bridges: E:Q.35, E:R.39, E:R.39, E:D.209, E:D.209 Salt bridges: E:R.39, E:H.252, E:H.252, E:R.256 UD2.17: 20 residues within 4Å: Chain F: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.16 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:Y.37 Hydrogen bonds: F:Q.35, F:N.64, F:N.93, F:N.93, F:R.98, F:R.98, F:D.114, F:D.114, F:D.114, F:D.115, F:D.115, F:Q.205, F:D.208, F:R.256 Water bridges: F:R.39, F:R.39, F:G.178 Salt bridges: F:R.39, F:H.252, F:H.252, F:R.256 UD2.20: 20 residues within 4Å: Chain G: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.19 24 PLIP interactions: 24 interactions with chain G Hydrophobic interactions: G:Y.37 Hydrogen bonds: G:Q.35, G:Y.37, G:N.64, G:N.93, G:N.93, G:R.98, G:R.98, G:D.114, G:D.114, G:D.115, G:D.115, G:G.178, G:Q.205, G:R.256 Water bridges: G:Q.35, G:R.39, G:R.39, G:D.209, G:D.209 Salt bridges: G:R.39, G:H.252, G:H.252, G:R.256 UD2.23: 20 residues within 4Å: Chain H: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, L.176, G.178, Q.205, N.206, D.208, D.209, H.252, R.256 Ligands: MN.22 22 PLIP interactions: 22 interactions with chain H Hydrophobic interactions: H:Y.37 Hydrogen bonds: H:Q.35, H:N.64, H:N.93, H:N.93, H:R.98, H:R.98, H:D.114, H:D.114, H:D.114, H:D.115, H:D.115, H:Q.205, H:D.208, H:R.256 Water bridges: H:R.39, H:R.39, H:G.178 Salt bridges: H:R.39, H:H.252, H:H.252, H:R.256

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

EDO.3: 7 residues within 4Å: Chain A: F.134, Q.137, P.223, I.226, I.277 Chain B: Q.133, F.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.137 Water bridges: A:Q.137, A:K.222, A:G.225, A:S.275 EDO.6: 6 residues within 4Å: Chain A: Q.133, F.134 Chain B: F.134, Q.137, P.223, I.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.137 Water bridges: B:Q.137, B:K.222, B:S.275 EDO.9: 7 residues within 4Å: Chain C: F.134, Q.137, P.223, I.226, I.277 Chain D: Q.133, F.134 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.137 Water bridges: C:Q.137, C:K.222, C:G.225, C:S.275 EDO.12: 6 residues within 4Å: Chain C: Q.133, F.134 Chain D: F.134, Q.137, P.223, I.277 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.137 Water bridges: D:Q.137, D:K.222, D:S.275 EDO.15: 7 residues within 4Å: Chain E: F.134, Q.137, P.223, I.226, I.277 Chain F: Q.133, F.134 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.137 Water bridges: E:Q.137, E:K.222, E:G.225, E:S.275 EDO.18: 6 residues within 4Å: Chain E: Q.133, F.134 Chain F: F.134, Q.137, P.223, I.277 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.137 Water bridges: F:Q.137, F:K.222, F:S.275 EDO.21: 7 residues within 4Å: Chain G: F.134, Q.137, P.223, I.226, I.277 Chain H: Q.133, F.134 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Q.137 Water bridges: G:Q.137, G:K.222, G:G.225, G:S.275 EDO.24: 6 residues within 4Å: Chain G: Q.133, F.134 Chain H: F.134, Q.137, P.223, I.277 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.137 Water bridges: H:Q.137, H:K.222, H:S.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedersen, L.C. et al., Crystal structure of an alpha-1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. J.Biol.Chem. (2003)

Release Date

2003-04-22

Peptides

Alpha-1,4-N-acetylhexosaminyltransferase EXTL2: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Alpha-1,4-N-acetylhexosaminyltransferase EXTL2

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