SMTL ID : 3nwk.2 (3 other biounits)

A second C2221 form of concanavalin A (Canavalia ensiformis)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:Y.12, A:D.19, H2O.1, H2O.2 CA.7: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.7, H2O.10 CA.11: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.10, H2O.11 CA.17: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.17, H2O.19

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

MN.2: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.3, H2O.5 MN.8: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.6, H2O.9 MN.12: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.12, H2O.15 MN.18: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.15, H2O.19

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228 GOL.4: 9 residues within 4Å: Chain A: S.113, N.124, A.125, L.126, V.179, H.180 Chain B: F.130, Q.137, D.139 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.137, B:D.139, A:H.180 Water bridges: A:N.124 GOL.5: 4 residues within 4Å: Chain A: N.44, S.201, D.203, S.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.44 Water bridges: A:S.201 GOL.6: 5 residues within 4Å: Chain A: V.170, I.221, S.223, G.224, T.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.224 Water bridges: A:V.170 GOL.9: 8 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.14, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100 Water bridges: B:R.228 GOL.10: 10 residues within 4Å: Chain A: F.130, Q.137, D.139 Chain B: S.113, L.115, N.124, A.125, L.126, V.179, H.180 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.137, A:D.139, B:H.180 Water bridges: B:N.124 GOL.13: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.14, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228 GOL.14: 9 residues within 4Å: Chain C: S.113, N.124, A.125, L.126, V.179, H.180 Chain D: F.130, Q.137, D.139 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.137, D:D.139, D:D.139, C:H.180 Water bridges: C:N.124 GOL.15: 4 residues within 4Å: Chain C: N.44, S.201, D.203, S.204 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.44 Water bridges: C:S.201 GOL.16: 5 residues within 4Å: Chain C: V.170, I.221, S.223, G.224, T.226 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.224 Water bridges: C:V.170 GOL.19: 8 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.14, D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100 Water bridges: D:R.228 GOL.20: 10 residues within 4Å: Chain C: F.130, Q.137, D.139 Chain D: S.113, L.115, N.124, A.125, L.126, V.179, H.180 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:H.180, C:Q.137, C:D.139, C:D.139 Water bridges: D:N.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Foroughi, L.M. et al., Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms. Cryst.Growth Des. (2011)

Release Date

2011-07-13

Peptides

Concanavalin-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
B

D
D

Concanavalin-A

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