SMTL ID : 4p14.1

Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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.9: 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.4, H2O.5 CA.17: 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.8, H2O.8 CA.25: 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.11, H2O.11

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.1, H2O.1 MN.10: 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.4, H2O.5 MN.18: 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.7, H2O.8 MN.26: 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.11, H2O.11

4 x ADE: ADENINE(Non-covalent)

ADE.3: 6 residues within 4Å: Chain A: Y.12, P.13, N.14, T.15, D.16, R.228 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.12, A:Y.12, A:N.14, A:T.15, A:D.16, A:D.16, A:R.228, A:R.228 ADE.11: 6 residues within 4Å: Chain B: Y.12, P.13, N.14, T.15, D.16, R.228 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.12, B:Y.12, B:N.14, B:T.15, B:D.16, B:D.16, B:R.228, B:R.228 ADE.19: 6 residues within 4Å: Chain C: Y.12, P.13, N.14, T.15, D.16, R.228 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.12, C:N.14, C:T.15, C:D.16, C:R.228, C:R.228 ADE.27: 6 residues within 4Å: Chain D: Y.12, P.13, N.14, T.15, D.16, R.228 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.12, D:N.14, D:T.15, D:D.16, D:R.228, D:R.228

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100 GOL.8: 4 residues within 4Å: Chain A: S.34, K.35, K.36, T.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.37, A:T.37 GOL.12: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.14, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100 GOL.16: 4 residues within 4Å: Chain B: S.34, K.35, K.36, T.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.37, B:T.37 GOL.20: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.14, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100 GOL.24: 4 residues within 4Å: Chain C: S.34, K.35, K.36, T.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.37, C:T.37 GOL.28: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.14, D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100 GOL.32: 4 residues within 4Å: Chain D: S.34, K.35, K.36, T.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.37, D:T.37

4 x DBB: D-ALPHA-AMINOBUTYRIC ACID(Non-covalent)

DBB.5: 11 residues within 4Å: Chain A: S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain D: M.129, F.130, Q.137, D.139 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:Q.137, D:D.139, D:D.139, A:A.125, A:A.125, A:H.180 Hydrophobic interactions: A:L.115 DBB.13: 11 residues within 4Å: Chain B: S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain C: M.129, F.130, Q.137, D.139 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.115 Hydrogen bonds: B:A.125, B:A.125, B:H.180, C:Q.137, C:D.139, C:D.139 DBB.21: 11 residues within 4Å: Chain B: M.129, F.130, Q.137, D.139 Chain C: S.113, L.115, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Q.137, B:D.139, C:A.125, C:A.125, C:H.180 Hydrophobic interactions: C:L.115 DBB.29: 11 residues within 4Å: Chain A: M.129, F.130, Q.137, D.139 Chain D: S.113, L.115, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.115 Hydrogen bonds: D:A.125, D:A.125, D:H.180, A:Q.137, A:D.139

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

EDO.6: 2 residues within 4Å: Chain A: Y.176 Chain D: R.90 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Y.176, D:R.90, D:R.90 EDO.7: 2 residues within 4Å: Chain A: Q.143, G.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.144 EDO.14: 2 residues within 4Å: Chain B: Y.176 Chain C: R.90 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.90, C:R.90, B:Y.176 EDO.15: 2 residues within 4Å: Chain B: Q.143, G.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.144 EDO.22: 2 residues within 4Å: Chain B: R.90 Chain C: Y.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.90, B:R.90 EDO.23: 2 residues within 4Å: Chain C: Q.143, G.144 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.144 EDO.30: 2 residues within 4Å: Chain A: R.90 Chain D: Y.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.90, A:R.90 EDO.31: 2 residues within 4Å: Chain D: Q.143, G.144 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delatorre, P. et al., Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine. To Be Published

Release Date

2015-04-15

Peptides

Concanavalin-Br: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Concanavalin-Br

Related Entries With Identical Sequence