SMTL ID : 1on6.2 (1 other biounit)

Crystal structure of mouse alpha-1,4-N-acetylhexosaminotransferase (EXTL2) in complex with UDPGlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: R.39, D.116 Ligands: UD1.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.116, H2O.3, H2O.4, H2O.4 MN.4: 4 residues within 4Å: Chain B: R.39, D.116, N.235 Ligands: UD1.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.116, H2O.7, H2O.8, H2O.8 MN.7: 3 residues within 4Å: Chain C: R.39, D.116 Ligands: UD1.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.116, H2O.10, H2O.12, H2O.12 MN.10: 4 residues within 4Å: Chain D: R.39, D.116, N.235 Ligands: UD1.11 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.116, H2O.14, H2O.15, H2O.15 MN.13: 3 residues within 4Å: Chain E: R.39, D.116 Ligands: UD1.14 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.116, H2O.18, H2O.19, H2O.20 MN.16: 4 residues within 4Å: Chain F: R.39, D.116, N.235 Ligands: UD1.17 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.116, H2O.22, H2O.23, H2O.23 MN.19: 3 residues within 4Å: Chain G: R.39, D.116 Ligands: UD1.20 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.116, H2O.26, H2O.27, H2O.27 MN.22: 4 residues within 4Å: Chain H: R.39, D.116, N.235 Ligands: UD1.23 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.116, H2O.30, H2O.31, H2O.31

8 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.2: 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, Y.156, L.176, G.178, N.206, D.208, D.209, H.252, R.256 Ligands: MN.1 26 PLIP interactions: 26 interactions with chain A 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.115, A:D.115, A:D.115, A:Y.156, A:G.178, A:D.208, A:D.209, A:R.256 Water bridges: A:Q.35, A:R.39, A:R.39, A:D.114, A:D.114, A:D.114, A:R.144 Salt bridges: A:R.39, A:H.252, A:H.252, A:R.256 UD1.5: 21 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, Y.156, L.176, G.178, N.206, C.207, D.208, D.209, H.252, R.256 Ligands: MN.4 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:L.176 Hydrogen bonds: B:Q.35, B:Y.37, B:N.64, B:N.93, B:N.93, B:R.98, B:R.98, B:D.114, B:D.115, B:D.115, B:G.178, B:C.207, B:D.208 Water bridges: B:Q.35, B:R.39, B:R.39, B:D.114, B:R.144 Salt bridges: B:R.39, B:H.252, B:H.252, B:R.256 UD1.8: 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, Y.156, L.176, G.178, N.206, D.208, D.209, H.252, R.256 Ligands: MN.7 26 PLIP interactions: 26 interactions with chain C 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.115, C:D.115, C:D.115, C:Y.156, C:G.178, C:D.208, C:D.209, C:R.256 Water bridges: C:Q.35, C:R.39, C:R.39, C:D.114, C:D.114, C:D.114, C:R.144 Salt bridges: C:R.39, C:H.252, C:H.252, C:R.256 UD1.11: 21 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, Y.156, L.176, G.178, N.206, C.207, D.208, D.209, H.252, R.256 Ligands: MN.10 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:L.176 Hydrogen bonds: D:Q.35, D:Y.37, D:N.64, D:N.93, D:N.93, D:R.98, D:R.98, D:D.114, D:D.115, D:D.115, D:G.178, D:C.207, D:D.208 Water bridges: D:Q.35, D:R.39, D:R.39, D:D.114, D:R.144 Salt bridges: D:R.39, D:H.252, D:H.252, D:R.256 UD1.14: 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, Y.156, L.176, G.178, N.206, D.208, D.209, H.252, R.256 Ligands: MN.13 26 PLIP interactions: 26 interactions with chain E 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.115, E:D.115, E:D.115, E:Y.156, E:G.178, E:D.208, E:D.209, E:R.256 Water bridges: E:Q.35, E:R.39, E:R.39, E:D.114, E:D.114, E:D.114, E:R.144 Salt bridges: E:R.39, E:H.252, E:H.252, E:R.256 UD1.17: 21 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, Y.156, L.176, G.178, N.206, C.207, D.208, D.209, H.252, R.256 Ligands: MN.16 23 PLIP interactions: 23 interactions with chain F Hydrophobic interactions: F:L.176 Hydrogen bonds: F:Q.35, F:Y.37, F:N.64, F:N.93, F:N.93, F:R.98, F:R.98, F:D.114, F:D.115, F:D.115, F:G.178, F:C.207, F:D.208 Water bridges: F:Q.35, F:R.39, F:R.39, F:D.114, F:R.144 Salt bridges: F:R.39, F:H.252, F:H.252, F:R.256 UD1.20: 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, Y.156, L.176, G.178, N.206, D.208, D.209, H.252, R.256 Ligands: MN.19 26 PLIP interactions: 26 interactions with chain G 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.115, G:D.115, G:D.115, G:Y.156, G:G.178, G:D.208, G:D.209, G:R.256 Water bridges: G:Q.35, G:R.39, G:R.39, G:D.114, G:D.114, G:D.114, G:R.144 Salt bridges: G:R.39, G:H.252, G:H.252, G:R.256 UD1.23: 21 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, Y.156, L.176, G.178, N.206, C.207, D.208, D.209, H.252, R.256 Ligands: MN.22 23 PLIP interactions: 23 interactions with chain H Hydrophobic interactions: H:L.176 Hydrogen bonds: H:Q.35, H:Y.37, H:N.64, H:N.93, H:N.93, H:R.98, H:R.98, H:D.114, H:D.115, H:D.115, H:G.178, H:C.207, H:D.208 Water bridges: H:Q.35, H:R.39, H:R.39, H:D.114, H:R.144 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: 7 residues within 4Å: Chain A: Q.133, F.134 Chain B: F.134, Q.137, P.223, I.226, I.277 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.137 Water bridges: B:K.222, B:K.222, B:G.225, 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: 7 residues within 4Å: Chain C: Q.133, F.134 Chain D: F.134, Q.137, P.223, I.226, I.277 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.137 Water bridges: D:K.222, D:K.222, D:G.225, 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: 7 residues within 4Å: Chain E: Q.133, F.134 Chain F: F.134, Q.137, P.223, I.226, I.277 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.137 Water bridges: F:K.222, F:K.222, F:G.225, 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: 7 residues within 4Å: Chain G: Q.133, F.134 Chain H: F.134, Q.137, P.223, I.226, I.277 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Q.137 Water bridges: H:K.222, H:K.222, H:G.225, 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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