SMTL ID : 4xtp.1

Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 4 residues within 4Å: Chain A: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.127, A:F.129, A:D.134, H2O.1, H2O.2 CA.13: 4 residues within 4Å: Chain B: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.127, B:F.129, B:D.134, H2O.7, H2O.7 CA.25: 4 residues within 4Å: Chain C: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.127, C:F.129, C:D.134, H2O.12, H2O.12 CA.37: 4 residues within 4Å: Chain D: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.127, D:F.129, D:D.134, H2O.17, H2O.17

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2: 4 residues within 4Å: Chain A: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.125, A:D.127, A:D.134, A:H.139, H2O.2, H2O.2 MN.14: 4 residues within 4Å: Chain B: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.125, B:D.127, B:D.134, B:H.139, H2O.7, H2O.7 MN.26: 4 residues within 4Å: Chain C: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.125, C:D.127, C:D.134, C:H.139, H2O.12, H2O.12 MN.38: 4 residues within 4Å: Chain D: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.125, D:D.127, D:D.134, D:H.139, H2O.17, H2O.17

4 x CIT: CITRIC ACID(Non-functional Binders)(Non-covalent)

CIT.3: 11 residues within 4Å: Chain A: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.138 Hydrogen bonds: A:T.87, A:T.87, A:T.128, A:T.128, A:R.138 Water bridges: A:R.138 Salt bridges: A:K.86, A:R.138, A:H.219 CIT.15: 11 residues within 4Å: Chain B: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.16 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:R.138 Hydrogen bonds: B:T.87, B:T.87, B:T.128, B:T.128, B:R.138 Water bridges: B:R.138 Salt bridges: B:K.86, B:R.138, B:H.219 CIT.27: 11 residues within 4Å: Chain C: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.28 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:R.138 Hydrogen bonds: C:T.87, C:T.87, C:T.128, C:T.128, C:R.138 Water bridges: C:R.138 Salt bridges: C:K.86, C:R.138, C:H.219 CIT.39: 11 residues within 4Å: Chain D: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.40 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:R.138 Hydrogen bonds: D:T.87, D:T.87, D:T.128, D:T.128, D:R.138 Water bridges: D:R.138 Salt bridges: D:K.86, D:R.138, D:H.219

28 x SO4: SULFATE ION(Non-covalent)(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: K.86, F.129, H.219 Ligands: CIT.3 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: N.131, T.132 Ligands: SER.11, A2G.12 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: K.40, R.217 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: R.217 Ligand excluded by PLIP SO4.8: 1 residues within 4Å: Chain A: Q.103 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: T.29, K.31, K.33 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: G.160, K.161, V.162, S.184 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: K.86, F.129, H.219 Ligands: CIT.15 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: N.131, T.132 Ligands: SER.23, A2G.24 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: K.40, R.217 Ligand excluded by PLIP SO4.19: 1 residues within 4Å: Chain B: R.217 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain B: Q.103 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: T.29, K.31, K.33 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: G.160, K.161, V.162, S.184 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: K.86, F.129, H.219 Ligands: CIT.27 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain C: N.131, T.132 Ligands: SER.35, A2G.36 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain C: K.40, R.217 Ligand excluded by PLIP SO4.31: 1 residues within 4Å: Chain C: R.217 Ligand excluded by PLIP SO4.32: 1 residues within 4Å: Chain C: Q.103 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: T.29, K.31, K.33 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain C: G.160, K.161, V.162, S.184 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain D: K.86, F.129, H.219 Ligands: CIT.39 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain D: N.131, T.132 Ligands: SER.47, A2G.48 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain D: K.40, R.217 Ligand excluded by PLIP SO4.43: 1 residues within 4Å: Chain D: R.217 Ligand excluded by PLIP SO4.44: 1 residues within 4Å: Chain D: Q.103 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain D: T.29, K.31, K.33 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain D: G.160, K.161, V.162, S.184 Ligand excluded by PLIP

4 x SER: SERINE(Non-functional Binders)(Non-covalent)

SER.11: 2 residues within 4Å: Ligands: SO4.5, A2G.12 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.11, S.11, S.11, S.11 SER.23: 2 residues within 4Å: Ligands: SO4.17, A2G.24 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.23, S.23, S.23, S.23 SER.35: 2 residues within 4Å: Ligands: SO4.29, A2G.36 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.35, S.35, S.35, S.35 SER.47: 2 residues within 4Å: Ligands: SO4.41, A2G.48 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.47, S.47, S.47, S.47

4 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)(Non-functional Binders)

A2G.12: 15 residues within 4Å: Chain A: A.88, D.89, D.105, G.106, G.107, F.108, F.129, N.131, W.133, G.214, L.215, S.216, H.219 Ligands: SO4.5, SER.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.108, A:W.133 Hydrogen bonds: A:D.89, A:G.107, A:N.131, A:L.215, A:S.216, A:H.219 A2G.24: 15 residues within 4Å: Chain B: A.88, D.89, D.105, G.106, G.107, F.108, F.129, N.131, W.133, G.214, L.215, S.216, H.219 Ligands: SO4.17, SER.23 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.108, B:W.133 Hydrogen bonds: B:D.89, B:G.107, B:N.131, B:L.215, B:S.216, B:H.219 A2G.36: 15 residues within 4Å: Chain C: A.88, D.89, D.105, G.106, G.107, F.108, F.129, N.131, W.133, G.214, L.215, S.216, H.219 Ligands: SO4.29, SER.35 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.108, C:W.133 Hydrogen bonds: C:D.89, C:G.107, C:N.131, C:L.215, C:S.216, C:S.216 A2G.48: 15 residues within 4Å: Chain D: A.88, D.89, D.105, G.106, G.107, F.108, F.129, N.131, W.133, G.214, L.215, S.216, H.219 Ligands: SO4.41, SER.47 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.108, D:W.133 Hydrogen bonds: D:D.89, D:G.107, D:N.131, D:L.215, D:S.216, D:S.216

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Sousa, B.L. et al., Crystal structure of a recombinant Vatairea macrocarpa seed lectin. Int.J.Biochem.Cell Biol. (2016)

Release Date

2016-01-27

Peptides

Seed lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Seed lectin

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