SMTL ID : 3usu.1 (1 other biounit)

Crystal structure of Butea monosperma seed lectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-FUC.1: 2 residues within 4Å: Chain A: F.117, N.118 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.3: 3 residues within 4Å: Chain C: V.116, N.118, S.120 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-FUC.2: 4 residues within 4Å: Chain B: V.116, N.118, S.120 Ligands: XYP.12 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.129, A:Y.131, A:D.138, H2O.2, H2O.2 CA.9: 4 residues within 4Å: Chain B: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.129, B:D.129, B:Y.131, H2O.5, H2O.5 CA.13: 4 residues within 4Å: Chain C: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.129, C:Y.131, C:D.138, H2O.6, H2O.7 CA.17: 4 residues within 4Å: Chain D: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.129, D:Y.131, D:D.138, H2O.9, H2O.9

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

MN.5: 5 residues within 4Å: Chain A: E.127, D.129, D.138, H.143, S.153 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.127, A:D.129, A:D.138, A:H.143, H2O.1, H2O.1 MN.10: 4 residues within 4Å: Chain B: E.127, D.129, D.138, H.143 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.129, B:D.138, B:H.143, H2O.3, H2O.5 MN.14: 4 residues within 4Å: Chain C: E.127, D.129, D.138, H.143 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.127, C:D.129, C:D.138, C:H.143, H2O.6, H2O.6 MN.18: 4 residues within 4Å: Chain D: E.127, D.129, D.138, H.143 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.127, D:D.129, D:D.138, D:H.143, H2O.8, H2O.9

4 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-functional Binders)(Non-covalent)

ABU.6: 10 residues within 4Å: Chain A: N.3, D.5, S.56, P.57, I.58, N.59, W.208, S.236, L.238 Chain D: N.18 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:D.5, A:I.58, A:N.59 Hydrogen bonds: A:D.5, A:P.57, A:L.238, D:N.18 ABU.11: 11 residues within 4Å: Chain B: N.3, T.4, D.5, P.57, I.58, N.59, W.208, S.236, K.237, L.238 Chain C: N.18 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:D.5, B:I.58, B:N.59 Hydrogen bonds: B:N.3, B:D.5, B:D.5, B:D.5, B:S.236, B:L.238, C:N.18 ABU.16: 9 residues within 4Å: Chain B: N.18 Chain C: T.4, D.5, S.56, P.57, I.58, N.59, S.236, L.238 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:D.5, C:I.58, C:N.59 Hydrogen bonds: C:S.56, C:S.56, C:N.59, B:N.18 Water bridges: C:T.4 ABU.20: 11 residues within 4Å: Chain A: F.7, T.8, F.9, K.13, Q.16, N.18 Chain D: N.3, T.4, D.5, N.59, W.208 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:N.3, A:F.9 Hydrogen bonds: D:N.3, D:D.5, D:D.5, D:N.59, A:Q.16 Water bridges: A:N.18 Salt bridges: A:K.13

4 x GOL: GLYCEROL(Non-covalent)(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: K.168, L.170, A.183 Chain B: T.172, V.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.168 GOL.8: 5 residues within 4Å: Chain A: T.172, V.181 Chain B: K.168, V.169, L.170 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.168, A:T.172 GOL.15: 8 residues within 4Å: Chain C: K.168, V.169, L.170, A.183, V.185, L.253 Chain D: L.170, V.181 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.168 GOL.19: 8 residues within 4Å: Chain C: L.170, T.172, V.181 Chain D: K.168, V.169, L.170, A.183, V.185 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.168, D:L.170, C:T.172, C:T.172

1 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.12: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-FUC.2, NAG-NAG-BMA-MAN-FUC.2, NAG-NAG-BMA-MAN-FUC.2 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain D: N.118, S.120 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.120

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Abhilash, J. et al., Crystal structure of Butea monosperma seed lectin. To be Published

Release Date

2012-01-04

Peptides

Lectin Alpha chain: AC
Lectin Beta Chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Lectin Alpha chain

Lectin Beta Chain

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