SMTL ID : 3r0g.1

3D Structure of Ferric Methanosarcina Acetivorans Protoglobin I149F mutant in Aquomet form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 23 residues within 4Å: Chain A: L.70, Y.73, F.74, Y.85, V.89, R.92, F.93, W.96, Y.112, I.116, R.119, H.120, K.125, N.126, I.137, Y.141, L.142, F.145, I.146, F.149, T.178, V.182, W.185 34 PLIP interactions: 33 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.73, A:F.74, A:F.74, A:V.89, A:V.89, A:R.92, A:F.93, A:F.93, A:W.96, A:W.96, A:I.116, A:I.137, A:I.137, A:Y.141, A:F.145, A:F.145, A:F.145, A:F.149, A:T.178, A:V.182 Hydrogen bonds: A:Y.85, A:R.92, A:Y.112, A:N.126, A:T.128 Water bridges: A:R.92, A:Q.127, A:T.128, A:T.128 Salt bridges: A:R.92, A:R.119 pi-Stacking: A:W.185 Metal complexes: A:H.120, H2O.1 HEM.6: 24 residues within 4Å: Chain B: L.70, Y.73, F.74, Y.85, V.89, R.92, F.93, W.96, Y.112, I.116, R.119, H.120, K.125, N.126, T.128, I.137, Y.141, L.142, F.145, I.146, F.149, T.178, V.182, W.185 32 PLIP interactions: 31 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.73, B:Y.73, B:F.74, B:F.74, B:Y.85, B:V.89, B:V.89, B:F.93, B:F.93, B:W.96, B:W.96, B:I.116, B:I.137, B:I.137, B:Y.141, B:F.145, B:F.145, B:F.145, B:F.149, B:T.178, B:V.182 Hydrogen bonds: B:R.92, B:N.126 Water bridges: B:R.92, B:Q.127, B:D.129, B:D.129 Salt bridges: B:R.92, B:R.119 pi-Stacking: B:W.185 Metal complexes: B:H.120, H2O.4

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.3: 4 residues within 4Å: Chain A: K.191, D.194 Chain B: H.121, R.122 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.121, A:K.191 Water bridges: B:T.123 GOL.4: 5 residues within 4Å: Chain A: L.27, E.30 Chain B: H.67, P.68, H.69 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.69, A:E.30

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 5 residues within 4Å: Chain A: P.19, F.20, N.21, D.24 Chain B: R.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.19

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 6 residues within 4Å: Chain A: H.121, R.122, T.123 Chain B: K.191, Y.192, D.194 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:T.123 Salt bridges: A:R.122, B:D.194 Hydrogen bonds: B:K.191, B:D.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pesce, A. et al., Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants. Iubmb Life (2011)

Release Date

2011-06-08

Peptides

Methanosarcina acetivorans protoglobin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methanosarcina acetivorans protoglobin

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