Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1K1E

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0009103	biological_process	lipopolysaccharide biosynthetic process
A	0016787	molecular_function	hydrolase activity
A	0016788	molecular_function	hydrolase activity, acting on ester bonds
A	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
A	0046872	molecular_function	metal ion binding
B	0009103	biological_process	lipopolysaccharide biosynthetic process
B	0016787	molecular_function	hydrolase activity
B	0016788	molecular_function	hydrolase activity, acting on ester bonds
B	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
B	0046872	molecular_function	metal ion binding
C	0009103	biological_process	lipopolysaccharide biosynthetic process
C	0016787	molecular_function	hydrolase activity
C	0016788	molecular_function	hydrolase activity, acting on ester bonds
C	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
C	0046872	molecular_function	metal ion binding
D	0009103	biological_process	lipopolysaccharide biosynthetic process
D	0016787	molecular_function	hydrolase activity
D	0016788	molecular_function	hydrolase activity, acting on ester bonds
D	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
D	0046872	molecular_function	metal ion binding
E	0009103	biological_process	lipopolysaccharide biosynthetic process
E	0016787	molecular_function	hydrolase activity
E	0016788	molecular_function	hydrolase activity, acting on ester bonds
E	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
E	0046872	molecular_function	metal ion binding
F	0009103	biological_process	lipopolysaccharide biosynthetic process
F	0016787	molecular_function	hydrolase activity
F	0016788	molecular_function	hydrolase activity, acting on ester bonds
F	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
F	0046872	molecular_function	metal ion binding
G	0009103	biological_process	lipopolysaccharide biosynthetic process
G	0016787	molecular_function	hydrolase activity
G	0016788	molecular_function	hydrolase activity, acting on ester bonds
G	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
G	0046872	molecular_function	metal ion binding
H	0009103	biological_process	lipopolysaccharide biosynthetic process
H	0016787	molecular_function	hydrolase activity
H	0016788	molecular_function	hydrolase activity, acting on ester bonds
H	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
H	0046872	molecular_function	metal ion binding
I	0009103	biological_process	lipopolysaccharide biosynthetic process
I	0016787	molecular_function	hydrolase activity
I	0016788	molecular_function	hydrolase activity, acting on ester bonds
I	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
I	0046872	molecular_function	metal ion binding
J	0009103	biological_process	lipopolysaccharide biosynthetic process
J	0016787	molecular_function	hydrolase activity
J	0016788	molecular_function	hydrolase activity, acting on ester bonds
J	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
J	0046872	molecular_function	metal ion binding
K	0009103	biological_process	lipopolysaccharide biosynthetic process
K	0016787	molecular_function	hydrolase activity
K	0016788	molecular_function	hydrolase activity, acting on ester bonds
K	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
K	0046872	molecular_function	metal ion binding
L	0009103	biological_process	lipopolysaccharide biosynthetic process
L	0016787	molecular_function	hydrolase activity
L	0016788	molecular_function	hydrolase activity, acting on ester bonds
L	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
L	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO A 201

Chain	Residue
A	ASP14
A	ASP16
A	ASP107
A	HOH2503
A	HOH2504
A	HOH2505

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO B 202

Chain	Residue
B	HOH2414
B	HOH2415
B	HOH2416
B	ASP14
B	ASP16
B	ASP107

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO C 203

Chain	Residue
C	ASP14
C	ASP16
C	ASP107
C	HOH2602
C	HOH2603
C	HOH2604

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO D 204

Chain	Residue
D	ASP14
D	ASP16
D	ASP107
D	HOH2405
D	HOH2406
D	HOH2407

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO E 205

Chain	Residue
E	ASP14
E	ASP16
E	ASP107
E	HOH2419
E	HOH2420
E	HOH2421

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO F 206

Chain	Residue
F	ASP14
F	ASP16
F	ASP107
F	HOH2416
F	HOH2417
F	HOH2418

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO G 207

Chain	Residue
G	ASP14
G	ASP16
G	ASP107
G	HOH2505
G	HOH2506
G	HOH2507

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO H 208

Chain	Residue
H	ASP14
H	ASP16
H	ASP107
H	HOH2603
H	HOH2604
H	HOH2605

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO I 209

Chain	Residue
I	ASP14
I	ASP16
I	ASP107
I	HOH2502
I	HOH2503
I	HOH2504

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO J 210

Chain	Residue
J	ASP14
J	ASP16
J	ASP107
J	HOH2604
J	HOH2605
J	HOH2606

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO K 211

Chain	Residue
K	ASP14
K	ASP16
K	ASP107
K	HOH2507
K	HOH2508
K	HOH2509

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO L 212

Chain	Residue
L	ASP14
L	ASP16
L	ASP107
L	HOH2413
L	HOH2414
L	HOH2415

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HG A 301

Chain	Residue
A	CYS88
A	TYR104
A	ALA114
A	CYS118

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE HG B 302

Chain	Residue
B	CYS88
B	ALA114
B	CYS118

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE HG C 303

Chain	Residue
C	CYS88
C	ALA114
C	CYS118

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HG D 304

Chain	Residue
D	CYS88
D	TYR104
D	ALA114
D	CYS118

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE HG E 305

Chain	Residue
E	CYS88
E	ALA114
E	CYS118

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HG F 306

Chain	Residue
F	CYS88
F	TYR104
F	ALA114
F	CYS118

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE HG G 307

Chain	Residue
G	CYS88
G	ALA114
G	CYS118

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HG H 308

Chain	Residue
H	CYS118
H	CYS88
H	TYR104
H	ALA114

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HG I 309

Chain	Residue
I	CYS88
I	TYR104
I	ALA114
I	CYS118

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HG J 310

Chain	Residue
J	CYS88
J	MET92
J	ALA114
J	CYS118

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE HG K 311

Chain	Residue
K	CYS88
K	ALA114
K	CYS118

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE HG L 312

Chain	Residue
L	CYS88
L	ALA114
L	CYS118

site_id	CC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE SO4 A 2401

Chain	Residue
A	ASP14
A	SER58
A	GLY59
A	LEU82
A	LYS84
A	VAL110
A	HOH2504
A	HOH2505
A	HOH2529
A	HOH2585
A	HOH2594
A	HOH2616

site_id	CC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 2402

Chain	Residue
B	ASP14
B	SER58
B	GLY59
B	LYS84
B	VAL110
B	HOH2415
B	HOH2444
B	HOH2513

site_id	CC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 C 2403

Chain	Residue
C	ASP14
C	SER58
C	GLY59
C	LYS84
C	VAL110
C	HOH2603
C	HOH2604
C	HOH2605
C	HOH2647
C	HOH2683
C	HOH2696

site_id	DC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 D 2404

Chain	Residue
D	ASP14
D	SER58
D	GLY59
D	ARG60
D	LYS84
D	VAL110
D	HOH2406
D	HOH2417
D	HOH2420

site_id	DC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 E 2405

Chain	Residue
E	ASP14
E	SER58
E	GLY59
E	LEU82
E	LYS84
E	VAL110
E	HOH2420
E	HOH2421
E	HOH2426
E	HOH2501

site_id	DC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 F 2406

Chain	Residue
F	ASP14
F	SER58
F	GLY59
F	LYS84
F	VAL110
F	HOH2417
F	HOH2430
F	HOH2490
F	HOH2494

site_id	DC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 G 2407

Chain	Residue
G	ASP14
G	SER58
G	GLY59
G	ARG60
G	LYS84
G	VAL110
G	HOH2506
G	HOH2507
G	HOH2509
G	HOH2578

site_id	DC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 H 2408

Chain	Residue
H	ASP14
H	SER58
H	GLY59
H	ARG60
H	LEU82
H	LYS84
H	VAL110
H	HOH2604
H	HOH2615
H	HOH2647

site_id	DC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 I 2409

Chain	Residue
I	ASP14
I	SER58
I	GLY59
I	LYS84
I	VAL110
I	HOH2503
I	HOH2504
I	HOH2505
I	HOH2514

site_id	DC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 J 2410

Chain	Residue
J	ASP14
J	SER58
J	GLY59
J	LEU82
J	LYS84
J	VAL110
J	HOH2605
J	HOH2638
J	HOH2652

site_id	DC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 K 2411

Chain	Residue
K	ASP14
K	SER58
K	GLY59
K	ARG60
K	LYS84
K	VAL110
K	HOH2508
K	HOH2509
K	HOH2512
K	HOH2578

site_id	DC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 L 2412

Chain	Residue
L	ASP14
L	SER58
L	GLY59
L	LYS84
L	VAL110
L	HOH2414
L	HOH2427
L	HOH2485

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 2413

Chain	Residue
B	THR167
B	ALA168
B	GLN169

site_id	EC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 2414

Chain	Residue
A	THR167
A	ALA168
A	GLN169

site_id	EC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 2415

Chain	Residue
F	THR167
F	ALA168
F	GLN169
F	HOH2518

site_id	EC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 I 2416

Chain	Residue
I	THR167
I	ALA168
I	GLN169

site_id	EC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 J 2417

Chain	Residue
J	THR167
J	ALA168
J	GLN169

site_id	EC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 2418

Chain	Residue
E	THR167
E	ALA168
E	GLN169

site_id	EC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE MES C 2601

Chain	Residue
A	HIS25
A	ILE33
B	GLN23
C	GLN23
C	ILE33
D	GLN23
D	HIS25
D	HOH2449
D	HOH2534

site_id	EC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MES H 2602

Chain	Residue
E	GLN23
E	HIS25
F	GLN23
G	GLN23
H	GLN23
H	HIS25
H	ILE33

site_id	EC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MES J 2603

Chain	Residue
I	GLN23
I	ILE33
J	HIS25
J	ILE33
K	GLN23
L	GLN23
L	HOH2454

site_id	FC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL I 2501

Chain	Residue
G	LYS75
G	LEU76
G	PHE77
G	GLN94
G	HOH2516
I	ASP90
I	LYS93
I	GLN94

site_id	FC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 2502

Chain	Residue
A	ASP90
A	LYS93
A	GLN94
D	LYS75
D	LEU76
D	PHE77
D	GLN94
D	HOH2438
D	HOH2463

site_id	FC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 2503

Chain	Residue
C	LYS75
C	LEU76
C	PHE77
C	ASP90
C	LYS93
C	GLN94
C	GLN94
C	HOH2636
C	HOH2703

site_id	FC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL G 2504

Chain	Residue
G	ASP90
G	LYS93
G	GLN94
I	LYS75
I	LEU76
I	PHE77
I	GLN94
I	HOH2601

site_id	FC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL K 2505

Chain	Residue
E	LYS75
E	LEU76
E	PHE77
E	GLN94
E	HOH2450
K	ASP90
K	LYS93
K	GLN94

site_id	FC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL K 2506

Chain	Residue
E	ASP90
E	LYS93
E	GLN94
K	LYS75
K	LEU76
K	PHE77
K	GLN94
K	HOH2528

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	BINDING: BINDING => ECO:0000305\|PubMed:11835514

Chain	Residue	Details
A	ASP14
E	ASP107
F	ASP14
F	ASP107
G	ASP14
G	ASP107
H	ASP14
H	ASP107
I	ASP14
I	ASP107
J	ASP14
A	ASP107
J	ASP107
K	ASP14
K	ASP107
L	ASP14
L	ASP107
B	ASP14
B	ASP107
C	ASP14
C	ASP107
D	ASP14
D	ASP107
E	ASP14

site_id	SWS_FT_FI2
Number of Residues	72
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P67653

Chain	Residue	Details
A	ASP16
B	ARG60
B	ARG68
B	LYS84
C	ASP16
C	HIS37
C	LYS45
C	ARG60
C	ARG68
C	LYS84
D	ASP16
A	HIS37
D	HIS37
D	LYS45
D	ARG60
D	ARG68
D	LYS84
E	ASP16
E	HIS37
E	LYS45
E	ARG60
E	ARG68
A	LYS45
E	LYS84
F	ASP16
F	HIS37
F	LYS45
F	ARG60
F	ARG68
F	LYS84
G	ASP16
G	HIS37
G	LYS45
A	ARG60
G	ARG60
G	ARG68
G	LYS84
H	ASP16
H	HIS37
H	LYS45
H	ARG60
H	ARG68
H	LYS84
I	ASP16
A	ARG68
I	HIS37
I	LYS45
I	ARG60
I	ARG68
I	LYS84
J	ASP16
J	HIS37
J	LYS45
J	ARG60
J	ARG68
A	LYS84
J	LYS84
K	ASP16
K	HIS37
K	LYS45
K	ARG60
K	ARG68
K	LYS84
L	ASP16
L	HIS37
L	LYS45
B	ASP16
L	ARG60
L	ARG68
L	LYS84
B	HIS37
B	LYS45

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)