SMTL ID : 4jj0.3 (2 other biounits)

Crystal structure of MamP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

8 x HEC: HEME C(Covalent)(Non-covalent)

HEC.1: 19 residues within 4Å: Chain A: P.210, I.213, A.217, K.218, M.219, P.220, H.221, R.224, G.225, P.226, C.227, C.230, H.231 Chain B: R.222 Chain C: P.182, Y.183 Chain D: P.175, G.176, C.187 14 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A, 2 interactions with chain C, Salt bridges: B:R.222, A:R.224 Hydrophobic interactions: A:P.210, A:I.213, A:M.219, A:P.220, A:R.224 Water bridges: A:R.224, A:R.224, A:R.224, C:Y.183 Metal complexes: A:H.221, A:H.231 Hydrogen bonds: C:Y.183 HEC.2: 18 residues within 4Å: Chain A: Q.63, S.65, A.170, P.171, I.173, D.177, I.178, M.179, P.180, H.181, R.184, G.185, P.186, C.187, C.190, H.191 Chain D: R.224 Ligands: GOL.3 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:A.170, A:P.171, A:I.173, A:I.173, A:D.177, A:M.179, A:P.180, A:R.184, D:R.224 Water bridges: A:R.184, A:R.184 Salt bridges: A:R.184 pi-Cation interactions: A:R.184 Metal complexes: A:H.181, A:H.191 HEC.4: 18 residues within 4Å: Chain A: R.222 Chain B: P.210, I.213, A.217, K.218, M.219, P.220, H.221, R.224, G.225, P.226, C.227, C.230, H.231 Chain C: P.175, G.176, C.187 Chain D: Y.183 14 PLIP interactions: 12 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: B:P.210, B:I.213, B:I.213, B:M.219, B:P.220, B:R.224 Water bridges: B:R.224, B:R.224 Salt bridges: B:R.224, A:R.222 pi-Cation interactions: B:R.224 Metal complexes: B:H.221, B:H.231 Hydrogen bonds: D:Y.183 HEC.5: 18 residues within 4Å: Chain B: Q.63, S.65, A.170, P.171, I.173, D.177, I.178, M.179, P.180, H.181, R.184, G.185, P.186, C.187, Q.189, C.190, H.191 Chain C: R.224 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:A.170, B:P.171, B:I.173, B:D.177, B:M.179, B:P.180, B:R.184 Water bridges: B:R.184, B:R.184, B:H.198, D:D.204 Salt bridges: B:R.184 pi-Cation interactions: B:R.184 Metal complexes: B:H.181, B:H.191 HEC.6: 19 residues within 4Å: Chain A: P.182, Y.183 Chain B: P.175, G.176, C.187 Chain C: P.210, I.213, A.217, K.218, M.219, P.220, H.221, R.224, G.225, P.226, C.227, C.230, H.231 Chain D: R.222 14 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D, 2 interactions with chain A, Hydrophobic interactions: C:P.210, C:I.213, C:M.219, C:P.220, C:R.224 Water bridges: C:R.224, C:R.224, C:R.224, A:Y.183 Salt bridges: C:R.224, D:R.222 Metal complexes: C:H.221, C:H.231 Hydrogen bonds: A:Y.183 HEC.7: 18 residues within 4Å: Chain B: R.224 Chain C: Q.63, S.65, A.170, P.171, I.173, D.177, I.178, M.179, P.180, H.181, R.184, G.185, P.186, C.187, C.190, H.191 Ligands: GOL.8 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:A.170, C:P.171, C:I.173, C:I.173, C:D.177, C:M.179, C:P.180, C:R.184, B:R.224 Water bridges: C:R.184, C:R.184 Salt bridges: C:R.184 pi-Cation interactions: C:R.184 Metal complexes: C:H.181, C:H.191 HEC.9: 18 residues within 4Å: Chain A: P.175, G.176, C.187 Chain B: Y.183 Chain C: R.222 Chain D: P.210, I.213, A.217, K.218, M.219, P.220, H.221, R.224, G.225, P.226, C.227, C.230, H.231 14 PLIP interactions: 12 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: D:P.210, D:I.213, D:I.213, D:M.219, D:P.220, D:R.224 Water bridges: D:R.224, D:R.224 Salt bridges: D:R.224, C:R.222 pi-Cation interactions: D:R.224 Metal complexes: D:H.221, D:H.231 Hydrogen bonds: B:Y.183 HEC.10: 18 residues within 4Å: Chain A: R.224 Chain D: Q.63, S.65, A.170, P.171, I.173, D.177, I.178, M.179, P.180, H.181, R.184, G.185, P.186, C.187, Q.189, C.190, H.191 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:A.170, D:P.171, D:I.173, D:D.177, D:M.179, D:P.180, D:R.184 Water bridges: D:R.184, D:R.184, D:R.184, D:H.198 Salt bridges: D:R.184 pi-Cation interactions: D:R.184 Metal complexes: D:H.181, D:H.191

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.171, M.172, I.173, L.174, D.177, H.198 Ligands: HEC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.172, A:L.174, A:D.177 GOL.8: 7 residues within 4Å: Chain C: P.171, M.172, I.173, L.174, D.177, H.198 Ligands: HEC.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.172, C:L.174, C:D.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Siponen, M.I. et al., Structural insight into magnetochrome-mediated magnetite biomineralization. Nature (2013)

Release Date

2013-10-09

Peptides

MamP: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

MamP

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