SMTL ID : 2xij.1

Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.1: 6 residues within 4Å: Chain A: A.127, A.150, Y.254, Q.342, L.386 Ligands: B12.13 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.342 Water bridges: A:S.104, A:A.150, A:R.218, A:Y.254, A:Y.254 5AD.14: 6 residues within 4Å: Chain B: A.127, A.150, Y.254, Q.342, L.386 Ligands: B12.26 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.342 Water bridges: B:S.104, B:A.150, B:R.218, B:E.382

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.603, R.604, R.606, D.634 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.604 Water bridges: A:R.606 Salt bridges: A:R.604, A:R.606 SO4.3: 3 residues within 4Å: Chain A: Y.136, N.140, R.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.140 Salt bridges: A:R.142 SO4.15: 4 residues within 4Å: Chain B: R.603, R.604, R.606, D.634 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.604 Salt bridges: B:R.604, B:R.606 SO4.16: 3 residues within 4Å: Chain B: Y.136, N.140, R.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.140 Salt bridges: B:R.142

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

EDO.4: 3 residues within 4Å: Chain A: S.584, K.585, E.586 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: E.55, D.262, I.264, L.435 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: K.410 Chain B: D.48, L.49, I.50, W.51 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: R.98, S.296, A.339, H.340, S.374 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: T.105, E.107, V.500, R.503, Q.504, K.507 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: S.175, M.176, T.177, T.206, I.207, Q.208, S.250 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: P.685, I.687, G.707 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: F.236, T.239, A.240, F.246, S.248, L.286, R.294 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: S.584, K.585, E.586 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: E.55, D.262, I.264, L.435 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: D.48, L.49, I.50, W.51 Chain B: K.410 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: R.98, S.296, A.339, H.340, S.374 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: T.105, E.107, V.500, R.503, Q.504, K.507 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: S.175, M.176, T.177, T.206, I.207, Q.208, S.250 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: P.685, I.687, G.707 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: F.236, T.239, A.240, F.246, S.248, L.286, R.294 Ligand excluded by PLIP

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.11: 9 residues within 4Å: Chain A: I.97, R.98, Q.99, Y.100, A.101, F.112, Q.121, S.125, R.396 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.99, A:Y.100, A:A.101, A:A.101, A:L.124, A:S.125, A:R.396, A:R.396 BTB.24: 9 residues within 4Å: Chain B: I.97, R.98, Q.99, Y.100, A.101, F.112, Q.121, S.125, R.396 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.99, B:Y.100, B:A.101, B:A.101, B:L.124, B:S.125, B:R.396, B:R.396

2 x B12: COBALAMIN(Non-covalent)

B12.13: 38 residues within 4Å: Chain A: F.128, L.130, H.133, A.150, V.217, R.218, T.220, E.258, A.259, G.345, W.346, E.382, A.383, L.384, G.385, Q.466, D.615, G.616, H.617, D.618, R.619, G.620, I.624, F.628, G.660, S.662, L.664, A.665, A.666, G.692, G.693, V.694, F.712, G.713, P.714, G.715, T.716 Ligands: 5AD.1 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:A.150, A:R.218, A:A.259, A:I.624, A:I.624, A:F.628, A:F.712, A:F.712 Hydrogen bonds: A:F.128, A:R.218, A:R.218, A:A.383, A:G.385, A:Q.466, A:D.615, A:G.616, A:H.617, A:D.618, A:D.618, A:D.618, A:R.619, A:G.620, A:A.665, A:G.693, A:G.715 Water bridges: A:F.128, A:N.219, A:N.219, A:W.346 Metal complexes: A:H.617 B12.26: 38 residues within 4Å: Chain B: F.128, L.130, H.133, A.150, V.217, R.218, T.220, E.258, A.259, G.345, W.346, E.382, A.383, L.384, G.385, Q.466, D.615, G.616, H.617, D.618, R.619, G.620, I.624, F.628, G.660, S.662, L.664, A.665, A.666, G.692, G.693, V.694, F.712, G.713, P.714, G.715, T.716 Ligands: 5AD.14 29 PLIP interactions: 29 interactions with chain B, Hydrophobic interactions: B:A.150, B:R.218, B:A.259, B:I.624, B:I.624, B:F.628, B:F.712, B:F.712 Hydrogen bonds: B:F.128, B:R.218, B:R.218, B:A.383, B:G.385, B:Q.466, B:G.616, B:H.617, B:D.618, B:D.618, B:R.619, B:G.620, B:A.665, B:G.693, B:G.715 Water bridges: B:F.128, B:N.219, B:N.219, B:W.346, B:E.382 Metal complexes: B:H.617

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Froese, D.S. et al., Structures of the Human Gtpase Mmaa and Vitamin B12-Dependent Methylmalonyl-Coa Mutase and Insight Into Their Complex Formation. J.Biol.Chem. (2010)

Release Date

2010-09-29

Peptides

METHYLMALONYL-COA MUTASE, MITOCHONDRIAL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

METHYLMALONYL-COA MUTASE, MITOCHONDRIAL

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