SMTL ID : 6xt6.1

pro-concanavalin A: Precursor of circularly permuted concanavalin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.142, D.144, D.153, H.158 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.142, A:D.144, A:D.153, A:H.158, H2O.1, H2O.1 MN.12: 5 residues within 4Å: Chain B: E.142, D.144, D.153, H.158, S.168 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.142, B:D.144, B:D.153, B:H.158, H2O.2, H2O.2 MN.24: 4 residues within 4Å: Chain C: E.142, D.144, D.153, H.158 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.142, C:D.144, C:D.153, C:H.158, H2O.4, H2O.4 MN.35: 5 residues within 4Å: Chain D: E.142, D.144, D.153, H.158, S.168 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.142, D:D.144, D:D.153, D:H.158, H2O.5, H2O.6

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.144, Y.146, N.148, D.153 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.144, A:Y.146, A:D.153, H2O.1, H2O.1 CA.4: 3 residues within 4Å: Chain A: H.62, E.65, E.221 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.65, A:E.221, H2O.1, H2O.1, H2O.3 CA.13: 4 residues within 4Å: Chain B: D.144, Y.146, N.148, D.153 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.144, B:Y.146, B:D.153, H2O.3, H2O.3 CA.15: 2 residues within 4Å: Chain B: E.253 Chain C: H.185 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.185, B:E.253, B:E.253, H2O.3, H2O.4 CA.25: 4 residues within 4Å: Chain C: D.144, Y.146, N.148, D.153 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.144, C:Y.146, C:D.153, H2O.4, H2O.5 CA.27: 3 residues within 4Å: Chain C: H.62, E.65, E.221 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.65, C:E.221, H2O.4, H2O.4, H2O.6 CA.36: 4 residues within 4Å: Chain D: D.144, Y.146, N.148, D.153 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.144, D:Y.146, D:D.153, H2O.6, H2O.6 CA.38: 2 residues within 4Å: Chain A: H.185 Chain D: E.253 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: D:E.253, D:E.253, A:H.185, H2O.6, H2O.7

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: K.193, D.214, D.216 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.214, A:D.214, A:D.216, A:D.216, H2O.1 ZN.14: 3 residues within 4Å: Chain B: K.193, D.214, D.216 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.214, B:D.216, B:D.216, H2O.3 ZN.26: 3 residues within 4Å: Chain C: K.193, D.214, D.216 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.214, C:D.214, C:D.216, C:D.216, H2O.4 ZN.37: 3 residues within 4Å: Chain D: K.193, D.214, D.216 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.214, D:D.216, D:D.216, H2O.6

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

EDO.5: 7 residues within 4Å: Chain A: L.8, V.61, H.62, A.71, S.247, L.249 Ligands: EDO.21 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: A.89, D.90, R.110, Y.146, N.148, G.232, L.233, Y.234 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: N.13, Q.14, D.33, G.34, N.35, L.241 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: V.213, D.214, N.217 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: H.9, E.74, A.75, T.76, S.244, F.245, T.246, T.259 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: M.11, F.12, Q.19, D.21 Chain B: N.6, A.7, H.62 Ligands: EDO.16 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: K.170, S.210, Y.211, D.212 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: V.61, H.62, A.71, S.247, K.248, L.249 Ligands: EDO.10 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: A.89, D.90, Y.146, G.232, L.233, Y.234 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: N.13, Q.14, G.34, N.35, L.241 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: V.213, D.214, N.217 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: H.9, E.74, A.75, T.76, S.244, F.245, T.246 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: N.6, A.7 Chain B: F.10, M.11, F.12, D.21, F.57 Ligands: EDO.5 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: I.23, L.24, Q.25 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: S.66, S.67, A.68 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain C: L.8, V.61, H.62, A.71, S.247, L.249 Ligands: EDO.44 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain C: A.89, D.90, R.110, Y.146, N.148, G.232, L.233, Y.234 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: N.13, Q.14, D.33, G.34, N.35, L.241 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: V.213, D.214, N.217 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain C: H.9, E.74, A.75, T.76, S.244, F.245, T.246, T.259 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain C: M.11, F.12, Q.19, D.21 Chain D: N.6, A.7, H.62 Ligands: EDO.39 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: K.170, S.210, Y.211, D.212 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain D: V.61, H.62, A.71, S.247, K.248, L.249 Ligands: EDO.33 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain D: A.89, D.90, Y.146, G.232, L.233, Y.234 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain D: N.13, Q.14, G.34, N.35, L.241 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain D: V.213, D.214, N.217 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: H.9, E.74, A.75, T.76, S.244, F.245, T.246 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain C: N.6, A.7 Chain D: F.10, M.11, F.12, D.21, F.57 Ligands: EDO.28 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain D: I.23, L.24, Q.25 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain D: S.66, S.67, A.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nonis, S.G. et al., Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase. Plant Cell (2021)

Release Date

2020-11-11

Peptides

Concanavalin-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Concanavalin-A