SMTL ID : 1nxd.5 (7 other biounits)

Crystal structure of MnMn Concanavalin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

16 x AZI: AZIDE ION(Non-covalent)

AZI.1: 4 residues within 4Å: Chain A: T.103, T.105, E.155, L.198 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.103, A:T.105, A:T.105, A:E.155 Water bridges: A:N.153, A:N.153 AZI.2: 7 residues within 4Å: Chain A: S.113, K.114, H.180, I.181, S.190, F.191 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.114, A:S.190, A:S.190, A:S.190 AZI.3: 7 residues within 4Å: Chain A: S.110, F.111, T.112, H.127, E.192, A.193, T.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.111, A:H.127, A:E.192, A:E.192 AZI.15: 2 residues within 4Å: Chain A: H.127 Chain B: H.127 No protein-ligand interaction detected (PLIP) AZI.16: 4 residues within 4Å: Chain B: K.138, L.140, I.141, Y.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.138, B:L.140 Water bridges: B:L.142 AZI.17: 3 residues within 4Å: Chain B: Y.12, P.13, H.205 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.13 Water bridges: B:Y.12, B:Y.12, B:H.205 AZI.18: 7 residues within 4Å: Chain A: W.88, N.124, H.180 Chain B: F.130, Q.137, D.139 Ligands: GOL.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.137, A:N.124, A:H.180 AZI.19: 5 residues within 4Å: Chain B: T.103, T.105, E.155, L.198, K.200 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.103, B:T.105, B:K.200, B:K.200 Water bridges: B:D.151, B:E.155 AZI.29: 4 residues within 4Å: Chain C: T.103, T.105, E.155, L.198 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.155 Water bridges: C:N.153, C:N.153, C:E.155, C:E.155 AZI.30: 7 residues within 4Å: Chain C: S.113, K.114, H.180, I.181, S.190, F.191 Ligands: GOL.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.114, C:H.180, C:S.190, C:S.190 AZI.31: 7 residues within 4Å: Chain C: S.110, F.111, T.112, H.127, E.192, A.193, T.194 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.112, C:T.112, C:T.194 AZI.43: 2 residues within 4Å: Chain C: H.127 Chain D: H.127 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.127 AZI.44: 4 residues within 4Å: Chain D: K.138, L.140, I.141, Y.176 1 PLIP interactions: 1 interactions with chain D Water bridges: D:L.142 AZI.45: 3 residues within 4Å: Chain D: Y.12, P.13, H.205 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.13 AZI.46: 7 residues within 4Å: Chain C: W.88, N.124, H.180 Chain D: F.130, Q.137, D.139 Ligands: GOL.38 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.124, C:H.180, D:Q.137 AZI.47: 5 residues within 4Å: Chain D: T.103, T.105, E.155, L.198, K.200 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.155, D:K.200 Water bridges: D:D.151, D:K.200

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

MN.4: 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.2, H2O.2 MN.5: 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.2, H2O.4 MN.20: 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.9, H2O.10 MN.21: 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.10, H2O.12 MN.32: 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.18, H2O.18 MN.33: 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.18, H2O.20 MN.48: 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.24, H2O.25 MN.49: 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.25, H2O.27

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: L.107, N.131 Chain B: E.122 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.122 Hydrogen bonds: A:L.107 NA.22: 3 residues within 4Å: Chain B: L.107, N.131, N.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.107 NA.34: 3 residues within 4Å: Chain C: L.107, N.131 Chain D: E.122 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.122 NA.50: 3 residues within 4Å: Chain D: L.107, N.131, N.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.153

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: N.44, S.201, D.203, S.204 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: A.1, P.222, S.223, P.234 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 Ligand excluded by PLIP GOL.10: 10 residues within 4Å: Chain A: S.113, N.124, A.125, L.126, V.179, H.180 Chain B: M.129, D.139 Ligands: AZI.2, AZI.18 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: Y.12, P.13, N.14, T.15, D.16 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: Q.143, G.144, S.220, I.221 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: A.38, S.72, A.73, T.74 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: K.138, L.140, I.141, Y.176 Chain B: P.178 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: A.38, K.39, S.72, A.73, T.74 Ligand excluded by PLIP GOL.24: 10 residues within 4Å: Chain A: D.139 Chain B: S.113, K.114, L.115, N.124, A.125, L.126, P.178, V.179, H.180 Ligand excluded by PLIP GOL.25: 11 residues within 4Å: Chain B: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: GOL.26 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain B: Y.12, L.99 Ligands: GOL.25 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: Q.143, G.144, S.220, I.221 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: R.228, L.229, P.234, D.235, A.236 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain C: N.44, S.201, D.203, S.204 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain C: A.1, P.222, S.223, P.234 Ligand excluded by PLIP GOL.37: 8 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 Ligand excluded by PLIP GOL.38: 10 residues within 4Å: Chain C: S.113, N.124, A.125, L.126, V.179, H.180 Chain D: M.129, D.139 Ligands: AZI.30, AZI.46 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain C: Y.12, P.13, N.14, T.15, D.16 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain C: Q.143, G.144, S.220, I.221 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain C: A.38, S.72, A.73, T.74 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain C: K.138, L.140, I.141, Y.176 Chain D: P.178 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain D: A.38, K.39, S.72, A.73, T.74 Ligand excluded by PLIP GOL.52: 10 residues within 4Å: Chain C: D.139 Chain D: S.113, K.114, L.115, N.124, A.125, L.126, P.178, V.179, H.180 Ligand excluded by PLIP GOL.53: 11 residues within 4Å: Chain D: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: GOL.54 Ligand excluded by PLIP GOL.54: 3 residues within 4Å: Chain D: Y.12, L.99 Ligands: GOL.53 Ligand excluded by PLIP GOL.55: 4 residues within 4Å: Chain D: Q.143, G.144, S.220, I.221 Ligand excluded by PLIP GOL.56: 5 residues within 4Å: Chain D: R.228, L.229, P.234, D.235, A.236 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Jaramillo, F.J. et al., Structure of concanavalin A at pH 8: bound solvent and crystal contacts. Acta Crystallogr.,Sect.D (2004)

Release Date

2004-03-30

Peptides

concanavalin A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
1

D
2

concanavalin A

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