- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 4 residues within 4Å:- Chain A: H.111, R.112, Y.113
- Chain D: R.409
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:H.111
SO4.8: 7 residues within 4Å:- Chain B: H.111, R.112, Y.113, P.114, Q.162
- Chain C: E.408, R.409
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:H.111
SO4.13: 5 residues within 4Å:- Chain B: E.408, R.409
- Chain C: H.111, R.112, Y.113
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.112
- Salt bridges: C:H.111
SO4.19: 6 residues within 4Å:- Chain A: E.408, R.409
- Chain D: H.111, R.112, Y.113, P.114
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Q.162
- Salt bridges: D:H.111
- 4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
SAM.3: 19 residues within 4Å:- Chain A: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, T.229, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298
- Ligands: LYS.4, SF4.6
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:H.131, A:T.133, A:T.133, A:Q.258, A:Q.258, A:D.293
- Water bridges: A:S.201, A:T.229
- Salt bridges: A:H.230
SAM.9: 19 residues within 4Å:- Chain B: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, R.202, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298
- Ligands: LYS.10, SF4.12
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:H.131, B:T.133, B:T.133, B:Q.258, B:Q.258, B:D.293
- Water bridges: B:S.201, B:T.229
- Salt bridges: B:H.230
SAM.15: 19 residues within 4Å:- Chain C: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, R.202, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298
- Ligands: LYS.16, SF4.18
9 PLIP interactions:9 interactions with chain C- Hydrogen bonds: C:H.131, C:T.133, C:G.171, C:Q.258, C:Q.258, C:D.293
- Water bridges: C:S.201, C:T.229
- Salt bridges: C:H.230
SAM.21: 20 residues within 4Å:- Chain D: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, R.202, T.229, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298
- Ligands: LYS.22, SF4.24
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:H.131, D:T.133, D:Q.258, D:Q.258, D:D.293
- Water bridges: D:S.201, D:T.229
- Salt bridges: D:H.230
- 4 x LYS: LYSINE(Non-covalent)
LYS.4: 12 residues within 4Å:- Chain A: L.98, L.118, T.133, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330
- Ligands: SAM.3, PLP.5
7 PLIP interactions:7 interactions with chain A,- Hydrophobic interactions: A:Y.290
- Hydrogen bonds: A:S.169, A:D.293, A:D.330
- Water bridges: A:R.198, A:Q.258
- Salt bridges: A:R.134
LYS.10: 11 residues within 4Å:- Chain B: L.98, L.118, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330
- Ligands: SAM.9, PLP.11
7 PLIP interactions:7 interactions with chain B,- Hydrophobic interactions: B:Y.290
- Hydrogen bonds: B:S.169, B:D.293, B:D.330
- Water bridges: B:Q.258, B:K.337
- Salt bridges: B:R.134
LYS.16: 12 residues within 4Å:- Chain C: L.98, L.118, T.133, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330
- Ligands: SAM.15, PLP.17
7 PLIP interactions:7 interactions with chain C,- Hydrophobic interactions: C:Y.290
- Hydrogen bonds: C:S.169, C:D.330
- Water bridges: C:R.198, C:Q.258, C:K.337
- Salt bridges: C:R.134
LYS.22: 11 residues within 4Å:- Chain D: L.98, L.118, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330
- Ligands: SAM.21, PLP.23
6 PLIP interactions:6 interactions with chain D,- Hydrophobic interactions: D:Y.290
- Hydrogen bonds: D:S.169, D:D.293
- Water bridges: D:Q.258, D:Y.290
- Salt bridges: D:R.134
- 4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)
PLP.5: 12 residues within 4Å:- Chain A: T.110, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337
- Chain B: S.320, G.321
- Ligands: LYS.4
13 PLIP interactions:11 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions- Hydrophobic interactions: A:T.110, A:Y.113, A:L.118, A:L.167, K.4
- Hydrogen bonds: A:R.112, B:G.321
- Water bridges: A:R.116, A:R.134, A:R.198
- Salt bridges: A:R.116, A:R.198, A:K.337
PLP.11: 13 residues within 4Å:- Chain A: S.320, G.321
- Chain B: T.110, R.112, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337
- Ligands: LYS.10
15 PLIP interactions:13 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A- Hydrophobic interactions: B:T.110, B:L.118, B:L.167, K.10
- Hydrogen bonds: B:R.112, A:G.321
- Water bridges: B:R.116, B:R.116, B:R.134, B:R.198, B:R.198, B:K.337
- Salt bridges: B:R.116, B:R.198, B:K.337
PLP.17: 12 residues within 4Å:- Chain C: T.110, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337
- Chain D: S.320, G.321
- Ligands: LYS.16
16 PLIP interactions:14 interactions with chain C, 1 interactions with chain D, 1 Ligand-Ligand interactions- Hydrophobic interactions: C:T.110, C:L.118, C:L.167, K.16
- Hydrogen bonds: C:R.112, C:Y.287, C:Y.288, D:G.321
- Water bridges: C:R.116, C:R.116, C:R.134, C:R.198, C:K.337
- Salt bridges: C:R.116, C:R.198, C:K.337
PLP.23: 13 residues within 4Å:- Chain C: S.320, G.321
- Chain D: T.110, R.112, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337
- Ligands: LYS.22
15 PLIP interactions:13 interactions with chain D, 1 Ligand-Ligand interactions, 1 interactions with chain C- Hydrophobic interactions: D:T.110, D:L.118, D:L.167, K.22
- Hydrogen bonds: D:R.112, D:Y.287, D:Y.288, C:G.321
- Water bridges: D:R.112, D:R.112, D:R.198, D:K.337
- Salt bridges: D:R.116, D:R.198, D:K.337
- 4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
SF4.6: 8 residues within 4Å:- Chain A: C.125, C.129, C.132, G.170, G.171, R.202, H.230
- Ligands: SAM.3
4 PLIP interactions:4 interactions with chain A,- Salt bridges: A:D.172
- Metal complexes: A:C.125, A:C.129, A:C.132
SF4.12: 8 residues within 4Å:- Chain B: C.125, C.129, C.132, G.170, G.171, R.202, H.230
- Ligands: SAM.9
4 PLIP interactions:4 interactions with chain B,- Salt bridges: B:D.172
- Metal complexes: B:C.125, B:C.129, B:C.132
SF4.18: 8 residues within 4Å:- Chain C: C.125, C.129, C.132, G.170, G.171, R.202, H.230
- Ligands: SAM.15
4 PLIP interactions:4 interactions with chain C,- Salt bridges: C:D.172
- Metal complexes: C:C.125, C:C.129, C:C.132
SF4.24: 9 residues within 4Å:- Chain D: C.125, Y.128, C.129, C.132, G.170, G.171, R.202, H.230
- Ligands: SAM.21
4 PLIP interactions:4 interactions with chain D,- Salt bridges: D:D.172
- Metal complexes: D:C.125, D:C.129, D:C.132
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lepore, B.W. et al., The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Proc.Natl.Acad.Sci.Usa (2005)
- Release Date
- 2005-10-04
- Peptides
- L-lysine 2,3-aminomutase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x SO4: SULFATE ION(Non-functional Binders)
- 4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
- 4 x LYS: LYSINE(Non-covalent)
- 4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)
- 4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lepore, B.W. et al., The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Proc.Natl.Acad.Sci.Usa (2005)
- Release Date
- 2005-10-04
- Peptides
- L-lysine 2,3-aminomutase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D