SMTL ID : 1on8.2 (1 other biounit)

Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with UDP and GlcUAb(1-3)Galb(1-O)-naphthalenelmethanol an acceptor substrate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-octamer

Ligands

8 x GAL- BDP: beta-D-glucopyranuronic acid-(1-3)-beta-D-galactopyranose(Non-covalent)

GAL-BDP.1: 9 residues within 4Å: Chain A: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Chain G: R.45 Ligands: UDP.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.144, A:Y.156, A:R.144 Water bridges: A:D.114, A:D.114, A:D.114, A:N.235, A:R.256 Salt bridges: A:R.144, A:H.252, A:R.256 GAL-BDP.2: 9 residues within 4Å: Chain B: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Chain F: R.45 Ligands: UDP.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:R.144, B:R.144, B:R.144, F:R.45 Water bridges: B:D.114, F:R.45 Salt bridges: B:R.144, B:H.252, B:R.256 GAL-BDP.9: 9 residues within 4Å: Chain C: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Chain E: R.45 Ligands: UDP.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.144, C:Y.156, C:R.144 Water bridges: C:D.114, C:D.114, C:D.114, C:N.235, C:R.256 Salt bridges: C:R.144, C:H.252, C:R.256 GAL-BDP.10: 9 residues within 4Å: Chain D: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Chain H: R.45 Ligands: UDP.15 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain H Hydrogen bonds: D:R.144, H:R.45, D:R.144, D:R.144 Water bridges: D:D.114, H:R.45 Salt bridges: D:R.144, D:H.252, D:R.256 GAL-BDP.17: 9 residues within 4Å: Chain A: R.45 Chain E: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Ligands: UDP.20 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.144, E:Y.156, E:R.144 Water bridges: E:D.114, E:D.114, E:D.114, E:N.235, E:R.256 Salt bridges: E:R.144, E:H.252, E:R.256 GAL-BDP.18: 9 residues within 4Å: Chain D: R.45 Chain F: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Ligands: UDP.23 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:R.144, D:R.45, F:R.144, F:R.144 Water bridges: F:D.114, D:R.45 Salt bridges: F:R.144, F:H.252, F:R.256 GAL-BDP.25: 9 residues within 4Å: Chain C: R.45 Chain G: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Ligands: UDP.28 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.144, G:Y.156, G:R.144 Water bridges: G:D.114, G:D.114, G:D.114, G:N.235, G:R.256 Salt bridges: G:R.144, G:H.252, G:R.256 GAL-BDP.26: 9 residues within 4Å: Chain B: R.45 Chain H: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Ligands: UDP.31 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain B Hydrogen bonds: H:R.144, B:R.45, H:R.144, H:R.144 Water bridges: H:D.114, B:R.45 Salt bridges: H:R.144, H:H.252, H:R.256

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

MN.3: 2 residues within 4Å: Chain A: D.116 Ligands: UDP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.116, H2O.1, H2O.1, H2O.1 MN.6: 3 residues within 4Å: Chain B: D.116, E.237 Ligands: UDP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.116, H2O.3, H2O.3, H2O.3 MN.11: 2 residues within 4Å: Chain C: D.116 Ligands: UDP.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.116, H2O.4, H2O.4, H2O.4 MN.14: 3 residues within 4Å: Chain D: D.116, E.237 Ligands: UDP.15 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.116, H2O.7, H2O.7, H2O.7 MN.19: 2 residues within 4Å: Chain E: D.116 Ligands: UDP.20 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.116, H2O.8, H2O.8, H2O.8 MN.22: 3 residues within 4Å: Chain F: D.116, E.237 Ligands: UDP.23 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.116, H2O.10, H2O.10, H2O.11 MN.27: 2 residues within 4Å: Chain G: D.116 Ligands: UDP.28 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.116, H2O.12, H2O.12, H2O.12 MN.30: 3 residues within 4Å: Chain H: D.116, E.237 Ligands: UDP.31 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.116, H2O.14, H2O.14, H2O.14

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

UDP.4: 17 residues within 4Å: Chain A: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, D.114, D.115, D.116, Y.243, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.1, MN.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.37, A:Y.243 Hydrogen bonds: A:Q.35, A:Y.37, A:R.39, A:N.64, A:N.93, A:N.93, A:D.115, A:D.115, A:Y.243, A:Y.243, A:M.246, A:W.247 Water bridges: A:R.39, A:R.39, A:D.114, A:D.114 Salt bridges: A:R.39 UDP.7: 19 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, Q.205, E.237, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.2, MN.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.37 Hydrogen bonds: B:Q.35, B:Y.37, B:N.64, B:N.93, B:N.93, B:R.98, B:D.114, B:D.115, B:D.115, B:Q.205, B:E.237, B:M.246, B:W.247 Water bridges: B:R.39, B:R.39, B:R.256 Salt bridges: B:R.39 UDP.12: 17 residues within 4Å: Chain C: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, D.114, D.115, D.116, Y.243, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.9, MN.11 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.37, C:Y.243 Hydrogen bonds: C:Q.35, C:Y.37, C:R.39, C:N.64, C:N.93, C:N.93, C:D.115, C:D.115, C:Y.243, C:Y.243, C:M.246, C:W.247 Water bridges: C:R.39, C:R.39, C:D.114, C:D.114 Salt bridges: C:R.39 UDP.15: 19 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, Q.205, E.237, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.10, MN.14 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.37 Hydrogen bonds: D:Q.35, D:Y.37, D:N.64, D:N.93, D:N.93, D:R.98, D:D.114, D:D.115, D:D.115, D:Q.205, D:E.237, D:M.246, D:W.247 Water bridges: D:R.39, D:R.39, D:R.256 Salt bridges: D:R.39 UDP.20: 17 residues within 4Å: Chain E: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, D.114, D.115, D.116, Y.243, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.17, MN.19 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:Y.37, E:Y.243 Hydrogen bonds: E:Q.35, E:Y.37, E:R.39, E:N.64, E:N.93, E:N.93, E:D.115, E:D.115, E:Y.243, E:Y.243, E:M.246, E:W.247 Water bridges: E:R.39, E:R.39, E:D.114, E:D.114 Salt bridges: E:R.39 UDP.23: 19 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, Q.205, E.237, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.18, MN.22 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:Y.37 Hydrogen bonds: F:Q.35, F:Y.37, F:N.64, F:N.93, F:N.93, F:R.98, F:D.114, F:D.115, F:D.115, F:Q.205, F:E.237, F:M.246, F:W.247 Water bridges: F:R.39, F:R.39, F:R.256 Salt bridges: F:R.39 UDP.28: 17 residues within 4Å: Chain G: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, D.114, D.115, D.116, Y.243, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.25, MN.27 19 PLIP interactions: 19 interactions with chain G Hydrophobic interactions: G:Y.37, G:Y.243 Hydrogen bonds: G:Q.35, G:Y.37, G:R.39, G:N.64, G:N.93, G:N.93, G:D.115, G:D.115, G:Y.243, G:Y.243, G:M.246, G:W.247 Water bridges: G:R.39, G:R.39, G:D.114, G:D.114 Salt bridges: G:R.39 UDP.31: 19 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, Q.205, E.237, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.26, MN.30 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:Y.37 Hydrogen bonds: H:Q.35, H:Y.37, H:N.64, H:N.93, H:N.93, H:R.98, H:D.114, H:D.115, H:D.115, H:Q.205, H:E.237, H:M.246, H:W.247 Water bridges: H:R.39, H:R.39, H:R.256 Salt bridges: H:R.39

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

EDO.5: 6 residues within 4Å: Chain A: F.134, Q.137, P.223, I.226, I.277 Chain B: Q.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.137 Water bridges: A:G.225 EDO.8: 6 residues within 4Å: Chain A: Q.133 Chain B: F.134, Q.137, P.223, I.226, I.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.137 Water bridges: B:Q.137, B:K.222, B:G.225 EDO.13: 6 residues within 4Å: Chain C: F.134, Q.137, P.223, I.226, I.277 Chain D: Q.133 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.137 Water bridges: C:G.225 EDO.16: 6 residues within 4Å: Chain C: Q.133 Chain D: F.134, Q.137, P.223, I.226, I.277 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.137 Water bridges: D:Q.137, D:K.222, D:G.225 EDO.21: 6 residues within 4Å: Chain E: F.134, Q.137, P.223, I.226, I.277 Chain F: Q.133 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.137 Water bridges: E:G.225 EDO.24: 6 residues within 4Å: Chain E: Q.133 Chain F: F.134, Q.137, P.223, I.226, I.277 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.137 Water bridges: F:Q.137, F:K.222, F:G.225 EDO.29: 6 residues within 4Å: Chain G: F.134, Q.137, P.223, I.226, I.277 Chain H: Q.133 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.137 Water bridges: G:G.225 EDO.32: 6 residues within 4Å: Chain G: Q.133 Chain H: F.134, Q.137, P.223, I.226, I.277 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.137 Water bridges: H:Q.137, H:K.222, H:G.225

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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