SMTL ID : 5e8m.1

Crystal structure of human heparanase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 5 residues within 4Å: Chain A: H.304, N.305, V.306, K.308 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.304, A:K.308, A:K.308, A:N.305

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: F.6, N.8, L.38 Chain B: I.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.8 NAG.3: 3 residues within 4Å: Chain A: T.40, N.46, S.48 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.40 Hydrogen bonds: A:S.48 NAG.4: 3 residues within 4Å: Chain A: D.29, N.63, F.104 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.104 NAG.5: 3 residues within 4Å: Chain A: L.43, N.84, Q.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84

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

EDO.6: 6 residues within 4Å: Chain A: Y.20, N.24, L.28, D.29, L.30, N.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.24, A:L.30 EDO.7: 6 residues within 4Å: Chain A: N.70, E.71, E.189 Chain B: D.30, G.64, T.65 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.65, B:T.65, A:N.70, A:E.189 Water bridges: B:D.30, B:T.65, B:K.66 EDO.8: 6 residues within 4Å: Chain A: F.256, V.260, G.261, T.262 Chain B: S.21 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.25 EDO.9: 3 residues within 4Å: Chain A: R.278, V.279, Y.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.279, A:V.279 Water bridges: A:R.278 EDO.10: 3 residues within 4Å: Chain A: R.220 Chain B: L.17, H.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.220, A:R.220, B:H.18 EDO.11: 6 residues within 4Å: Chain A: G.261, T.262, N.285, T.286, D.287 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.262, A:T.286, A:D.287 Water bridges: A:T.262 EDO.12: 3 residues within 4Å: Chain A: E.71, Y.144, Y.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.71, A:K.78 EDO.13: 5 residues within 4Å: Chain A: D.241, D.245, P.246, K.337, S.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.246 EDO.14: 2 residues within 4Å: Chain A: E.177, P.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.177 EDO.15: 3 residues within 4Å: Chain A: K.97, R.100, K.101 No protein-ligand interaction detected (PLIP) EDO.16: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.331 EDO.17: 4 residues within 4Å: Chain A: R.327, G.333, L.334, A.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.327 EDO.18: 5 residues within 4Å: Chain A: K.273, H.304, K.308 Chain B: V.7 Ligands: NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.308 EDO.19: 8 residues within 4Å: Chain A: L.54, C.57, S.58, Y.62, I.64, W.66, S.102, F.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.62, A:S.102, A:S.102 EDO.23: 4 residues within 4Å: Chain A: C.25 Chain B: P.46, R.49, R.53 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.49, B:R.53 Water bridges: B:R.53

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 3 residues within 4Å: Chain A: G.115, Q.116, H.142 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: G.233, A.234 Chain B: D.30, L.33 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain A: N.84, G.85, M.124, S.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, L. et al., Structural characterization of human heparanase reveals insights into substrate recognition. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-11-18

Peptides

Heparanase: A
Heparanase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparanase

Heparanase

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